diff -Nru r-bioc-biobase-2.14.0/DESCRIPTION r-bioc-biobase-2.20.0/DESCRIPTION --- r-bioc-biobase-2.14.0/DESCRIPTION 2011-11-01 04:27:52.000000000 +0000 +++ r-bioc-biobase-2.20.0/DESCRIPTION 2013-04-04 06:39:20.000000000 +0000 @@ -1,26 +1,24 @@ Package: Biobase Title: Biobase: Base functions for Bioconductor -Version: 2.14.0 +Version: 2.20.0 Author: R. Gentleman, V. Carey, M. Morgan, S. Falcon Description: Functions that are needed by many other packages or which replace R functions. Suggests: tools, tkWidgets, ALL -Depends: R (>= 2.10), utils -Imports: methods +Depends: R (>= 2.10), BiocGenerics (>= 0.3.2), utils +Imports: methods, BiocGenerics Maintainer: Bioconductor Package Maintainer License: Artistic-2.0 Collate: tools.R strings.R environment.R vignettes.R packages.R AllGenerics.R VersionsClass.R VersionedClasses.R methods-VersionsNull.R methods-VersionedClass.R DataClasses.R - methods-aggregator.R methods-ANY.R methods-container.R - methods-data.frame.R methods-matrix.R methods-phenoData.R - methods-MIAxE.R methods-MIAME.R methods-annotatedDataset.R - methods-AssayData.R methods-AnnotatedDataFrame.R methods-eSet.R + methods-aggregator.R methods-container.R methods-MIAxE.R + methods-MIAME.R methods-AssayData.R + methods-AnnotatedDataFrame.R methods-eSet.R methods-ExpressionSet.R methods-MultiSet.R methods-SnpSet.R - methods-NChannelSet.R anyMissing.R methods-exprSet.R - rowOp-methods.R updateObject.R updateObjectTo.R - methods-ScalarObject.R zzz.R + methods-NChannelSet.R anyMissing.R rowOp-methods.R + updateObjectTo.R methods-ScalarObject.R zzz.R LazyLoad: yes biocViews: Infrastructure, Bioinformatics -Packaged: 2011-11-01 04:27:52 UTC; biocbuild +Packaged: 2013-04-04 06:39:20 UTC; biocbuild diff -Nru r-bioc-biobase-2.14.0/NAMESPACE r-bioc-biobase-2.20.0/NAMESPACE --- r-bioc-biobase-2.14.0/NAMESPACE 2011-10-31 23:32:01.000000000 +0000 +++ r-bioc-biobase-2.20.0/NAMESPACE 2013-04-03 22:22:36.000000000 +0000 @@ -2,10 +2,16 @@ import(methods) -exportClasses(aggregator, container, eSet, phenoData, +importFrom(BiocGenerics, + combine, + updateObject, updateObjectFromSlots, getObjectSlots, + annotation, "annotation<-" +) + +exportClasses(aggregator, container, eSet, MIAxE, MIAME, characterORMIAME, annotatedDataset, AssayData, data.frameOrNULL, - exprSet, AnnotatedDataFrame, + AnnotatedDataFrame, Versions, VersionsNull, Versioned, VersionedBiobase, ExpressionSet, MultiSet, SnpSet, NChannelSet, ScalarObject, ScalarInteger, ScalarLogical, ScalarNumeric, @@ -14,23 +20,24 @@ exportMethods("[", "[[", "$", abstract, aggenv, aggfun, annotatedDataFrameFrom, annotation, channel, channelNames, coerce, - combine, content, contents, description, dims, eList, - experimentData, expinfo, exprs, + combine, content, contents, description, dimnames, "dimnames<-", + dims, experimentData, expinfo, exprs, featureNames, featureData, fData, fvarLabels, fvarMetadata, - geneNames, getExpData, hybridizations, initfun, - length, locked, makeDataPackage, normControls, notes, otherInfo, pData, + length, locked, makeDataPackage, normControls, notes, otherInfo, + pData, phenoData, preproc, protocolData, sampleNames, samples, se.exprs, selectChannels, snpCall, snpCallProbability, storageMode, varLabels, varMetadata, - "annotation<-", "description<-", "dimLabels<-", "eList<-", + "annotation<-", "description<-", "dimLabels<-", "experimentData<-", "exprs<-", - "featureNames<-", "featureData<-", "fData<-", "fvarLabels<-", "fvarMetadata<-", - "geneNames<-", "notes<-", "preproc<-", "pData<-", + "featureNames<-", "featureData<-", "fData<-", "fvarLabels<-", + "fvarMetadata<-", + "notes<-", "preproc<-", "pData<-", "phenoData<-", "protocolData<-", "sampleNames<-", "snpCall<-", "snpCallProbability<-", "varLabels<-", "varMetadata<-", "assayData<-", "se.exprs<-", "storageMode<-", - "write.exprs", dim, dimLabels, assayData, reporterNames, "reporterNames<-", + "write.exprs", dim, dimLabels, assayData, pubMedIds, "pubMedIds<-", isVersioned, isCurrent, classVersion, "classVersion<-", updateObject, updateObjectTo, @@ -53,13 +60,12 @@ "assayDataNew", "assayDataValidMembers", assayDataElementNames, assayDataElement, assayDataElementReplace, "assayDataElement<-", - "biocReposList", "cache", "copyEnv", "copySubstitute", "getObjectSlots", - "createPackage", "df2pD", "dumpPackTxt", "esApply", - "getPkgVigs", "isUnique", "l2e", "listLen", "matchpt", "mkScalar", + "cache", "copyEnv", "copySubstitute", + "createPackage", "dumpPackTxt", "esApply", + "getPkgVigs", "isUnique", "listLen", "matchpt", "mkScalar", "multiassign", "note", "openPDF","openVignette", "package.version", "reverseSplit", "rowMax", "rowMedians", "rowMin", "rowQ", - read.exprSet, read.phenoData, read.pD, readExpressionSet, read.AnnotatedDataFrame, read.MIAME, MIAME, "selectSome", "strbreak", "subListExtract", "testBioCConnection", "lcSuffix", "lcPrefix", "lcPrefixC", - "updateOldESet", "updateObjectFromSlots", "userQuery", "validMsg") + "updateOldESet", "userQuery", "validMsg") diff -Nru r-bioc-biobase-2.14.0/NEWS r-bioc-biobase-2.20.0/NEWS --- r-bioc-biobase-2.14.0/NEWS 2011-10-31 23:32:01.000000000 +0000 +++ r-bioc-biobase-2.20.0/NEWS 2013-04-03 22:22:36.000000000 +0000 @@ -1,3 +1,23 @@ +CHANGES IN VERSION 2.19 +----------------------- + +USER VISIBLE CHANGES + + o dimnames(), rownames(), colnames() and setters work on + eSet-derived objects + +CHANGES IN VERSION 2.17 +----------------------- + +USER VISIBLE CHANGES + + o l2e(), previously deprecated, has been made defunct. + + o All objects made defunct in previous release cycles have been removed. + This includes geneNames, getExpData, eList, reporterNames, getBiocRepos, + read.exprSet, updateOldMiame, df2pD, read.pD, read.phenoData, exprData, + exprList, and phenoData. + CHANGES IN VERSION 2.11 ---------------------- diff -Nru r-bioc-biobase-2.14.0/R/AllGenerics.R r-bioc-biobase-2.20.0/R/AllGenerics.R --- r-bioc-biobase-2.14.0/R/AllGenerics.R 2011-10-31 23:31:56.000000000 +0000 +++ r-bioc-biobase-2.20.0/R/AllGenerics.R 2013-04-03 22:22:27.000000000 +0000 @@ -1,33 +1,22 @@ setGeneric("abstract", function(object) standardGeneric("abstract")) setGeneric("aggenv", function(object) standardGeneric("aggenv")) setGeneric("aggfun", function(object) standardGeneric("aggfun")) -setGeneric("annotation", function(object) standardGeneric("annotation")) -setGeneric("annotation<-", function(object, value) standardGeneric("annotation<-")) setGeneric("annotatedDataFrameFrom", function(object, byrow, ...) standardGeneric("annotatedDataFrameFrom")) setGeneric("assayData", function(object)standardGeneric("assayData")) setGeneric("assayData<-", function(object, value) standardGeneric("assayData<-")) setGeneric("channelNames", function(object, ...) standardGeneric("channelNames")) setGeneric("channel", function(object, name, ...) standardGeneric("channel")) -setGeneric("combine", - function(x, y, ...) { - if (length(list(...)) > 0) { - callGeneric(x, do.call(callGeneric, - list(y, ...))) - } else { - standardGeneric("combine") - } - }) setGeneric("content", function(object) standardGeneric("content")) setGeneric("description", function(object, ...) standardGeneric("description")) setGeneric("description<-", function(object, value) standardGeneric("description<-")) setGeneric("dims", function(object) standardGeneric("dims")) +setGeneric("dimnames") +setGeneric("dimnames<-") setGeneric("dimLabels", function(object) standardGeneric("dimLabels")) setGeneric("dimLabels<-", function(object, value) standardGeneric("dimLabels<-")) setGeneric("esApply", function(X, MARGIN, FUN, ...) standardGeneric("esApply"), signature=c("X")) -setGeneric("eList", function(object) standardGeneric("eList")) -setGeneric("eList<-", function(object, value) standardGeneric("eList<-")) setGeneric("experimentData", function(object) standardGeneric("experimentData")) setGeneric("experimentData<-",function(object, value) standardGeneric("experimentData<-")) setGeneric("expinfo", function(object) standardGeneric("expinfo")) @@ -43,9 +32,6 @@ setGeneric("fvarLabels<-", function(object, value) standardGeneric("fvarLabels<-")) setGeneric("fvarMetadata", function(object) standardGeneric("fvarMetadata")) setGeneric("fvarMetadata<-", function(object, value) standardGeneric("fvarMetadata<-")) -setGeneric("geneNames", function(object) standardGeneric("geneNames")) -setGeneric("geneNames<-", function(object, value) standardGeneric("geneNames<-")) -setGeneric("getExpData", function(object, name) standardGeneric("getExpData")) setGeneric("hybridizations", function(object) standardGeneric("hybridizations")) setGeneric("initfun", function(object) standardGeneric("initfun")) setGeneric("locked", function(object) standardGeneric("locked")) @@ -70,8 +56,6 @@ setGeneric("protocolData<-", function(object, value) standardGeneric("protocolData<-")) setGeneric("pubMedIds", function(object) standardGeneric("pubMedIds")) setGeneric("pubMedIds<-", function(object, value) standardGeneric("pubMedIds<-")) -setGeneric("reporterNames", function(object) standardGeneric("reporterNames")) -setGeneric("reporterNames<-", function(object, value) standardGeneric("reporterNames<-")) setGeneric("sampleNames", function(object) standardGeneric("sampleNames")) setGeneric("sampleNames<-", function(object, value) standardGeneric("sampleNames<-")) setGeneric("samples", function(object) standardGeneric("samples")) @@ -95,13 +79,7 @@ setGeneric("classVersion<-", function(object, value) standardGeneric("classVersion<-")) setGeneric("isCurrent", function(object, value) standardGeneric("isCurrent")) setGeneric("isVersioned", function(object) standardGeneric("isVersioned")) -## updateObject -setGeneric("updateObject", - function(object, ..., verbose=FALSE) { - result <- standardGeneric("updateObject") - validObject(result) - result - }) +## updateObjectTo setGeneric("updateObjectTo", function(object, template, ..., verbose=FALSE) { result <- standardGeneric("updateObjectTo") diff -Nru r-bioc-biobase-2.14.0/R/DataClasses.R r-bioc-biobase-2.20.0/R/DataClasses.R --- r-bioc-biobase-2.14.0/R/DataClasses.R 2011-10-31 23:31:56.000000000 +0000 +++ r-bioc-biobase-2.20.0/R/DataClasses.R 2013-04-03 22:22:27.000000000 +0000 @@ -40,7 +40,10 @@ varMetadata = "data.frame" ), contains="Versioned", - validity = function(object) "class phenoData is defunct, convert using as(<>, \"AnnotatedDataFrame\")" + validity = function(object) { + paste("class phenoData is defunct,", + "convert using as(<>, \"AnnotatedDataFrame\")") + } ) # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - setOldClass("data.frame") @@ -197,7 +200,9 @@ notes = "character" ), contains = c("annotatedDataset"), # contains VersionedBiobase implicitly - validity = function(object) "class exprSet is defunct, convert using as(<>, \"ExpressionSet\")" + validity = function(object) + paste("class exprSet is defunct,", + "convert using as(<>, \"ExpressionSet\")") ) # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -Nru r-bioc-biobase-2.14.0/R/environment.R r-bioc-biobase-2.20.0/R/environment.R --- r-bioc-biobase-2.14.0/R/environment.R 2011-10-31 23:31:56.000000000 +0000 +++ r-bioc-biobase-2.20.0/R/environment.R 2013-04-03 22:22:27.000000000 +0000 @@ -45,31 +45,6 @@ BioC$Base <- Base options("BioC"=BioC) } -# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -biocReposList <- function() { - msg <- c(" The biocReposList() function is deprecated. ", - "Please use biocLite() to install\n packages:\n", - " source(\"http://bioconductor.org/biocLite.R\")\n", - " biocLite(\"\")\n", - " If you really need to get the list of Bioconductor package ", - "repositories (like\n biocReposList() does), then do:\n", - " source(\"http://bioconductor.org/biocLite.R\")\n", - " biocinstallRepos()\n") - .Deprecated(msg=msg) - ## Locations of Bioconductor release repositories - VERSION <- "2.9" - bioc_topurl <- getOption("BioC")$Base$urls$bioc - if (is.null(bioc_topurl)) - bioc_topurl <- "http://bioconductor.org" - pkg_topurl <- paste(bioc_topurl, "packages", VERSION, sep="/") - mkurl <- function(...) paste(pkg_topurl, ..., sep="/") - reposList <- c(bioc=mkurl("bioc"), - aData=mkurl("data/annotation"), - eData=mkurl("data/experiment"), - extra=mkurl("extra"), - cran="http://cran.fhcrc.org") - reposList -} # ========================================================================== # RG: # multiput and multiget @@ -130,9 +105,5 @@ ## Deprecated in v 2.11.2 l2e <- function(vals, envir) { - .Deprecated(msg="'l2e' is deprecated, use 'list2env' instead ") - if (missing(envir)) - list2env(vals, hash=TRUE) - else - list2env(vals, envir, hash=TRUE) + .Defunct("list2env", package="base") } diff -Nru r-bioc-biobase-2.14.0/R/methods-ANY.R r-bioc-biobase-2.20.0/R/methods-ANY.R --- r-bioc-biobase-2.14.0/R/methods-ANY.R 2011-10-31 23:31:56.000000000 +0000 +++ r-bioc-biobase-2.20.0/R/methods-ANY.R 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -setMethod("combine", - signature=signature( - x="ANY", y="missing"), - function(x, y, ...) x) diff -Nru r-bioc-biobase-2.14.0/R/methods-AnnotatedDataFrame.R r-bioc-biobase-2.20.0/R/methods-AnnotatedDataFrame.R --- r-bioc-biobase-2.14.0/R/methods-AnnotatedDataFrame.R 2011-10-31 23:31:56.000000000 +0000 +++ r-bioc-biobase-2.20.0/R/methods-AnnotatedDataFrame.R 2013-04-03 22:22:27.000000000 +0000 @@ -1,37 +1,48 @@ setMethod("initialize", signature(.Object="AnnotatedDataFrame"), - function(.Object, data = data.frame(), varMetadata = data.frame(),...) { - tryCatch({ - if (missing(varMetadata)) { - if (!missing(data)) checkClass(data, "data.frame", class(.Object)) - varMetadata <- data.frame(labelDescription = rep(NA, ncol(data))) - row.names(varMetadata) <- as.character(colnames(data)) - } else { - checkClass(varMetadata, "data.frame", class(.Object)) - if (!"labelDescription" %in% colnames(varMetadata)) - varMetadata[["labelDescription"]] <- rep(NA, nrow(varMetadata)) - row.names(varMetadata) <- names(data) - } - varMetadata[["labelDescription"]] <- as.character(varMetadata[["labelDescription"]]) - }, error=function(err) { - stop(conditionMessage(err), - "\n AnnotatedDataFrame 'initialize' could not update varMetadata:", - "\n perhaps pData and varMetadata are inconsistent?") - }) - callNextMethod(.Object, data=data, varMetadata=varMetadata, ...) - }) + function(.Object, data = data.frame(), varMetadata = data.frame(), + ...) +{ + tryCatch({ + if (missing(varMetadata)) { + if (!missing(data)) checkClass(data, "data.frame", class(.Object)) + varMetadata <- data.frame(labelDescription = rep(NA, ncol(data))) + row.names(varMetadata) <- as.character(colnames(data)) + } else { + checkClass(varMetadata, "data.frame", class(.Object)) + if (!"labelDescription" %in% colnames(varMetadata)) + varMetadata[["labelDescription"]] <- + rep(NA, nrow(varMetadata)) + row.names(varMetadata) <- names(data) + } + varMetadata[["labelDescription"]] <- + as.character(varMetadata[["labelDescription"]]) + }, error=function(err) { + stop(conditionMessage(err), + "\n AnnotatedDataFrame 'initialize' could not update varMetadata:", + "\n perhaps pData and varMetadata are inconsistent?") + }) + callNextMethod(.Object, data=data, varMetadata=varMetadata, ...) +}) -validAnnotatedDataFrame <- function( object ) { +validAnnotatedDataFrame <- function( object ) +{ msg <- NULL if (!is(object, "AnnotatedDataFrame")) - msg <- paste(msg, paste("Cannot validate", class(object), "as AnnotatedDataFrame" ), sep = "\n ") - if (length(row.names(varMetadata(object))) != length(colnames(pData(object)))) - msg <- paste(msg, "All AnnotatedDataFrame pData column names must be present as rows in varMetadata, and vice versa", sep="\n") + msg <- c(msg, paste("cannot validate", class(object), + "as AnnotatedDataFrame" )) + if (length(row.names(varMetadata(object))) != + length(colnames(pData(object)))) + msg <- c(msg, paste("all AnnotatedDataFrame pData column names", + "must be present as rows in varMetadata", + "and vice versa")) else if (any(row.names(varMetadata(object)) != colnames(pData(object)))) - msg <- paste(msg, "AnnotatedDataFrame colnames of data differ from row.names of varMetadata", sep="\n ") + msg <- c(msg, paste("AnnotatedDataFrame colnames of data differ", + "from row.names of varMetadata")) if ( !("labelDescription" %in% colnames(varMetadata(object)))) - msg <- paste(msg, "AnnotatedDataFrame varMetadata missing labelDescription column", sep="\n ") + msg <- c(msg, paste("AnnotatedDataFrame varMetadata", + "missing labelDescription column")) if (length(dimLabels(object))!=2) - msg <- paste(msg, "dimLabels must be a character vector of length 2", sep="\n ") + msg <- c(msg, "dimLabels must be a character vector of length 2") if (is.null(msg)) TRUE else msg } @@ -136,16 +147,19 @@ initialize(object, data=value, varMetadata=varMetadata) }) -setMethod("sampleNames", "AnnotatedDataFrame", function(object) row.names(object@data)) +setMethod("sampleNames", "AnnotatedDataFrame", + function(object) row.names(object@data)) -setReplaceMethod("sampleNames", c("AnnotatedDataFrame", "ANY"), function(object, value) { - if (length(value) != dim(object@data)[[1]]) - stop(paste("number of new names (", - length(value), - ") should equal number of rows in AnnotatedDataFrame (", - dim( object )[[1]], ")",sep="")) - row.names(object@data) <- value - object +setReplaceMethod("sampleNames", + signature(object="AnnotatedDataFrame", value="ANY"), + function(object, value) +{ + if (length(value) != dim(object@data)[[1]]) + stop("number of new names (", length(value), ") ", + "should equal number of rows in AnnotatedDataFrame (", + dim( object )[[1]], ")") + row.names(object@data) <- value + object }) setMethod("featureNames", @@ -161,15 +175,17 @@ setMethod("varLabels", "AnnotatedDataFrame", function(object) colnames(object@data)) -setReplaceMethod("varLabels", c("AnnotatedDataFrame", "ANY"), function(object, value) { - if (length(value) != dim(object@data)[[2]]) - stop(paste("number of new varLabels (", - length(value), - ") should equal number of columns in AnnotatedDataFrame (", - dim(object)[[2]], ")", sep="")) - colnames(object@data) <- value - row.names(object@varMetadata) <- value - object +setReplaceMethod("varLabels", + signature("AnnotatedDataFrame", "ANY"), + function(object, value) +{ + if (length(value) != dim(object@data)[[2]]) + stop("number of new varLabels (", length(value), ") ", + "should equal number of columns in AnnotatedDataFrame (", + dim(object)[[2]], ")") + colnames(object@data) <- value + row.names(object@varMetadata) <- value + object }) setMethod("varMetadata", "AnnotatedDataFrame", @@ -181,20 +197,23 @@ if (!("labelDescription" %in% colnames(value))) warning("'varMetadata' must have column 'labelDescription'") rinfo <- .row_names_info(value) - if (0L <= rinfo) { - ## not 'automatic' - bad <- setdiff(row.names(value), varLabels(object)) - if (length(bad)) { - fmt <- "'%s' not in 'varLabels()'" - stop(sprintf(fmt, paste(selectSome(bad), collapse="', '"))) + if (0L != length(varLabels(object))) { + if (0L <= rinfo) { + ## not 'automatic' + bad <- setdiff(row.names(value), varLabels(object)) + if (0L != length(bad)) { + fmt <- "'%s' not in 'varLabels()'" + nms <- paste(selectSome(bad), collapse="', '") + stop(sprintf(fmt, nms)) + } } + if (ncol(object) != abs(rinfo)) { + fmt <- "varMetadata has %d row(s), 'value' has %d" + stop(sprintf(fmt, ncol(object), nrow(value))) + } + if (0 < ncol(pData(object))) + row.names(value) <- names(pData(object)) } - if (ncol(object) != abs(rinfo)) { - fmt <- "varMetadata has %d row(s); 'value' has %d" - stop(sprintf(fmt, ncol(object), nrow(value))) - } - if (0 < ncol(pData(object))) - row.names(value) <- names(pData(object)) object@varMetadata <- value object }) @@ -313,8 +332,7 @@ .showAnnotatedDataFrame <- function(object, labels=list(0)) { - lbls <- list(object=paste("An object of class \"", - class(object), "\"", sep=""), + lbls <- list(object=paste0("An object of class '", class(object), "'"), sampleNames=dimLabels(object)[[1]], varMetadata="varMetadata", varLabels="varLabels") @@ -353,16 +371,16 @@ signature(x="AnnotatedDataFrame", y="AnnotatedDataFrame"), function(x, y) { if (class(x) != class(y)) { - msg <- sprintf("'%s' objects have diffrenent classes '%s', '%s'", - "combine,AnnotatedDataFrame,AnnotatedDataFrame-method", - class(x), class(y)) - stop(msg) + fmt <- "'%s' objects have diffrenent classes '%s', '%s'" + txt0 <- "combine,AnnotatedDataFrame,AnnotatedDataFrame-method" + stop(sprintf(fmt, txt0, class(x), class(y))) } if (!identical(dimLabels(x),dimLabels(y))) { - msg <- sprintf("AnnotatedDataFrame dimLabels differ:\n %s\n %s\n try 'updateObject'?", - paste(dimLabels(x), collapse=", "), - paste(dimLabels(y), collapse=", ")) - stop(msg) + fmt <- paste("AnnotatedDataFrame dimLabels differ:\n", + " %s\n", + " %s\n try 'updateObject'?") + stop(sprintf(fmt, paste(dimLabels(x), collapse=", "), + paste(dimLabels(y), collapse=", "))) } pDataX <- pData(x) @@ -371,7 +389,8 @@ varMetadataX <- varMetadata(x) varMetadataY <- varMetadata(y) - ## labelDescription is required, likely a factor with conflicting levels + ## labelDescription is required, likely a factor with + ## conflicting levels if (is.factor(varMetadataX$labelDescription) && is.factor(varMetadataY$labelDescription)) { f <- factor(c(as.character(varMetadataX$labelDescription), @@ -414,7 +433,7 @@ row.names=row.names, comment.char=varMetadata.char, ...) ## read varMetadata section (the lines with leading "#") - vmd = grep(paste("^", varMetadata.char, sep=""), + vmd = grep(paste0("^", varMetadata.char), readLines(filename), value=TRUE) svmd = strsplit(vmd, ":") varNames = sub("^# *", "", sapply(svmd, "[", 1L)) @@ -443,7 +462,7 @@ function(data, varMetadata, dimLabels=c("rowNames", "columnNames"), ...) { AnnotatedDataFrame(data=data.frame(), varMetadata=data.frame(), - dimLabels=dimLabels) + dimLabels=dimLabels, ...) }) setMethod("AnnotatedDataFrame", @@ -468,7 +487,7 @@ varMetadata[["labelDescription"]] <- as.character(varMetadata[["labelDescription"]]) new("AnnotatedDataFrame", data=data, varMetadata=varMetadata, - dimLabels=dimLabels) + dimLabels=dimLabels, ...) }) diff -Nru r-bioc-biobase-2.14.0/R/methods-AssayData.R r-bioc-biobase-2.20.0/R/methods-AssayData.R --- r-bioc-biobase-2.14.0/R/methods-AssayData.R 2011-10-31 23:31:56.000000000 +0000 +++ r-bioc-biobase-2.20.0/R/methods-AssayData.R 2013-04-03 22:22:27.000000000 +0000 @@ -1,19 +1,29 @@ -assayDataNew <- function(storage.mode = c("lockedEnvironment", "environment", "list"), ...) { - storage.mode <- match.arg(storage.mode) ## defaults to "lockedEnvironment" - assayData <- switch(storage.mode, - lockedEnvironment =, - environment = new.env(parent=emptyenv()), - list = list()) - - arglist <- list(...) - if( (length(arglist)>0L) && ((is.null(names(arglist))) || any(names(arglist)==""))) - stop("One or more arguments of this function are not named - please provide named arguments!") - - for (nm in names(arglist)) assayData[[nm]] <- arglist[[nm]] - if (storage.mode == "lockedEnvironment") assayDataEnvLock(assayData) - msg <- assayDataValidMembers(assayData) - if (!is.logical(msg)) stop(msg) - assayData +assayDataNew <- + function(storage.mode = c("lockedEnvironment", "environment", "list"), + ...) +{ + storage.mode <- match.arg(storage.mode) ## defaults to "lockedEnvironment" + assayData <- switch(storage.mode, + lockedEnvironment =, + environment = new.env(parent=emptyenv()), + list = list()) + + arglist <- list(...) + if((length(arglist)>0L) && + ((is.null(names(arglist))) || any(names(arglist)==""))) + stop("all arguments must be named") + + for (nm in names(arglist)) { + elt <- arglist[[nm]] + if (!is.null(dimnames(elt))) + dimnames(elt) <- lapply(dimnames(elt), unname) + assayData[[nm]] <- elt + } + if (storage.mode == "lockedEnvironment") + assayDataEnvLock(assayData) + msg <- assayDataValidMembers(assayData) + if (!is.logical(msg)) stop(msg) + assayData } assayDataValidMembers <- function(assayData, required) { @@ -24,17 +34,16 @@ if (!missing(required)) { absent <- required[!required %in% eltNames] if (length(absent) != 0) - msg <- paste(msg, - paste("'AssayData' missing '", absent ,"'" , sep = "", collapse = "\n\t"), - sep="\n") + msg <- c(msg, paste0("'AssayData' missing '", absent ,"'" , + collapse = "\n\t")) } dimsOk <- sapply(eltNames, function(elt) tryCatch(length(dim(assayData[[elt]]))>1, error=function(err) FALSE)) if (!all(dimsOk)) - msg <- c(msg, paste("'AssayData' elements with invalid dimensions: '", - paste(eltNames[!dimsOk], collapse="' '"), "'", sep="")) + msg <- c(msg, paste0("'AssayData' elements with invalid dimensions: '", + paste(eltNames[!dimsOk], collapse="' '"), "'")) if (length(assayData)>1) { eltRowNames <- rownames(assayData[[eltNames[[1]]]]) rowNamesOk <- @@ -90,7 +99,7 @@ else ls(object) if (!all(elts %in% names)) stop("'AssayData' missing elements: '", - paste(elts[!elts %in% names], collapse="', '", sep=""), "'") + paste0(elts[!elts %in% names], collapse="', '"), "'") switch(storageMode, lockedEnvironment = { assayData <- new.env(parent = emptyenv()) @@ -130,30 +139,6 @@ safe.colnames(object[[ls(object)[1]]])) }) -setReplaceMethod("sampleNames", c("AssayData", "ANY"), function(object, value) { - dims <- - switch(assayDataStorageMode(object), - lockedEnvironment=, - environment = eapply(object, ncol), - list = lapply(object, ncol)) - if (length(dims)==0 && length(value) !=0) - return(object) # early exit; no samples to name - if (!all(dims==length(value))) - stop("'value' length (", length(value), - ") must equal sample number in AssayData (",dims[[1]], ")") - switch(assayDataStorageMode(object), - lockedEnvironment = { - object <- copyEnv(object) - for (nm in ls(object)) colnames(object[[nm]]) <- value - assayDataEnvLock(object) - }, - environment = for (nm in ls(object)) colnames(object[[nm]]) <- value, - list = for (nm in names(object)) colnames(object[[nm]]) <- value - ) - object -}) - - setReplaceMethod("sampleNames", signature=signature( object="AssayData", @@ -186,6 +171,41 @@ object }) +setReplaceMethod("sampleNames", + signature(object="AssayData", value="ANY"), + function(object, value) +{ + dims <- + switch(assayDataStorageMode(object), + lockedEnvironment=, + environment = eapply(object, ncol), + list = lapply(object, ncol)) + if (length(dims)==0 && length(value) !=0) + return(object) # early exit; no samples to name + if (!all(dims==length(value))) + stop("'value' length (", length(value), + ") must equal sample number in AssayData (",dims[[1]], ")") + switch(assayDataStorageMode(object), + lockedEnvironment = { + object <- copyEnv(object) + for (nm in ls(object)) + colnames(object[[nm]]) <- value + assayDataEnvLock(object) + }, + environment = { + for (nm in ls(object)) + colnames(object[[nm]]) <- value + }, + list = { + for (nm in names(object)) + colnames(object[[nm]]) <- value + }) + object +}) + + + + setMethod("featureNames", signature(object="AssayData"), function(object) { if (!length(object)) @@ -227,8 +247,8 @@ nmfunc <- if ("environment"==class(x)) ls else names if (assayDataStorageMode(y) != storage.mode) - stop(paste("assayData must have same storage, but are ", - storage.mode, ", ", assayDataStorageMode(y), sep="")) + stop("assayData must have same storage, but are '", + storage.mode, "', '", assayDataStorageMode(y)) if (length(nmfunc(x)) != length(nmfunc(y))) stop("assayData have different numbers of elements:\n\t", paste(nmfunc(x), collapse=" "), "\n\t", diff -Nru r-bioc-biobase-2.14.0/R/methods-ExpressionSet.R r-bioc-biobase-2.20.0/R/methods-ExpressionSet.R --- r-bioc-biobase-2.14.0/R/methods-ExpressionSet.R 2011-10-31 23:31:56.000000000 +0000 +++ r-bioc-biobase-2.20.0/R/methods-ExpressionSet.R 2013-04-03 22:22:27.000000000 +0000 @@ -110,23 +110,12 @@ function(object, value) assayDataElementReplace(object, "exprs", value)) -setMethod("geneNames", signature(object="ExpressionSet"), - function(object) { - .Defunct("featureNames", "Biobase") - }) -setReplaceMethod("geneNames", signature(object="ExpressionSet", - value="character"), - function(object, value) { - .Defunct("featureNames<-", "Biobase") - }) - - .esApply <- function(X, MARGIN, FUN, ...) { parent <- environment(FUN) if (is.null(parent)) parent <- emptyenv() e1 <- new.env(parent=parent) - multiassign(names(pData(X)), pData(X), env=e1) + multiassign(names(pData(X)), pData(X), envir=e1) environment(FUN) <- e1 apply(exprs(X), MARGIN, FUN, ...) } @@ -149,7 +138,7 @@ VERSION=as.character(package_version(packageVersion)), LICENSE=license, TITLE = paste("Experimental Data Package:",packageName), - MAINTAINER = paste(author, ", <", email, ">", sep = ""), + MAINTAINER = paste0(author, ", <", email, ">"), BVIEWS = biocViews, DESCRIPTION = description, FORMAT = pD2Rd(phenoData(object))) @@ -161,7 +150,7 @@ ##save the data file datadir = file.path(res$pkgdir, "data") dir.create(datadir, showWarnings=FALSE) - outfile = file.path(datadir, paste(packageName, ".rda", sep="")) + outfile = file.path(datadir, paste0(packageName, ".rda")) assign(packageName, object) save(list=packageName, file = outfile) @@ -280,5 +269,3 @@ featureData=featureData, experimentData=experimentData, annotation=annotation, protocolData=protocolData, ...) }) - - diff -Nru r-bioc-biobase-2.14.0/R/methods-MIAME.R r-bioc-biobase-2.20.0/R/methods-MIAME.R --- r-bioc-biobase-2.14.0/R/methods-MIAME.R 2011-10-31 23:31:56.000000000 +0000 +++ r-bioc-biobase-2.20.0/R/methods-MIAME.R 2013-04-03 22:22:27.000000000 +0000 @@ -1,7 +1,3 @@ -updateOldMiame <- function(x) { - .Defunct("updateObject", "Biobase") -} - setMethod("isCurrent", signature(object="MIAME", value="missing"), function(object, value) { cver <- callNextMethod() @@ -20,7 +16,7 @@ if (isVersioned(object) && isCurrent(object)["MIAME"]) callNextMethod() else - updateObjectFromSlots(object, ..., verbose=verbose) + object <- updateObjectFromSlots(object, ..., verbose=verbose) classVersion(object) <- classVersion(class(object)) object }) diff -Nru r-bioc-biobase-2.14.0/R/methods-NChannelSet.R r-bioc-biobase-2.20.0/R/methods-NChannelSet.R --- r-bioc-biobase-2.14.0/R/methods-NChannelSet.R 2011-10-31 23:31:56.000000000 +0000 +++ r-bioc-biobase-2.20.0/R/methods-NChannelSet.R 2013-04-03 22:22:27.000000000 +0000 @@ -37,37 +37,40 @@ }) setValidity("NChannelSet", - function(object) { - msg <- validMsg(NULL, isValidVersion(object, "NChannelSet")) - if (!"channel" %in% names(varMetadata(object))) { - msg <- validMsg(msg, - "\n 'NChannelSet' varMetadata must have a 'channel' column") - } else { - channel <- - varMetadata(object)[["channel"]] - if (!is(channel, "factor")) - msg <- validMsg(msg, - "\n 'NChannelSet' varMetadata column 'channel' must be class 'factor'") - else if (0 < length(channel)) { - phenoChannels <- unique(channel) - phenoChannels <- phenoChannels[!is.na(phenoChannels)] - okChannels <- - phenoChannels %in% c("_ALL_", channelNames(object)) - if (!all(okChannels)) { - txt <- paste("\n 'NChannelSet' varMetadata 'channel' entries not in assayData: '", - paste(phenoChannels[!okChannels], - collapse="', '", sep=""), - "'", sep="") - msg <- validMsg(msg, txt) - } - - } - if (!("_ALL_" %in% levels(channel))) - msg <- validMsg(msg, - "\n 'NChannelSet' varMetadata 'channel' requires '_ALL_' as a level") - } - if (is.null(msg)) TRUE else msg - }) + function(object) +{ + msg <- validMsg(NULL, isValidVersion(object, "NChannelSet")) + if (!"channel" %in% names(varMetadata(object))) { + txt <- "\n 'NChannelSet' varMetadata must have a 'channel' column" + msg <- validMsg(msg, txt) + } else { + channel <- + varMetadata(object)[["channel"]] + if (!is(channel, "factor")) { + txt <- paste("\n 'NChannelSet' varMetadata column 'channel'", + "must be class 'factor'") + msg <- validMsg(msg, txt) + } else if (0 < length(channel)) { + phenoChannels <- unique(channel) + phenoChannels <- phenoChannels[!is.na(phenoChannels)] + okChannels <- + phenoChannels %in% c("_ALL_", channelNames(object)) + if (!all(okChannels)) { + txt0 <- paste0(phenoChannels[!okChannels], collapse="', '") + txt <- paste0("\n 'NChannelSet' varMetadata ", + "'channel' entries not in assayData: '", + txt0, "'") + msg <- validMsg(msg, txt) + } + } + if (!("_ALL_" %in% levels(channel))) { + txt <- paste("\n 'NChannelSet' varMetadata 'channel'", + "requires '_ALL_' as a level") + msg <- validMsg(msg, txt) + } + } + if (is.null(msg)) TRUE else msg +}) setMethod("channelNames", signature = signature( @@ -81,7 +84,7 @@ function(object, name, ...) { if (length(name) != 1) stop("\n 'NChannelSet' channel 'name' must be one element", - "\n was: '", paste(name, sep="", collapse="', '"), "'") + "\n was: '", paste0(name, collapse="', '"), "'") obj <- selectChannels(object, name) # subset phenoData appropriately sampleNames(phenoData(obj)) <- sampleNames(assayData(obj)) new("ExpressionSet", diff -Nru r-bioc-biobase-2.14.0/R/methods-VersionedClass.R r-bioc-biobase-2.20.0/R/methods-VersionedClass.R --- r-bioc-biobase-2.14.0/R/methods-VersionedClass.R 2011-10-31 23:31:56.000000000 +0000 +++ r-bioc-biobase-2.20.0/R/methods-VersionedClass.R 2013-04-03 22:22:27.000000000 +0000 @@ -29,7 +29,7 @@ vers[is.na(vers)] <- FALSE names(vers) <- nm bad <- names(vers[vers==FALSE]) - msg <- validMsg(msg, paste("out-of-date class version '", bad, "'", sep="")) + msg <- validMsg(msg, paste0("out-of-date class version '", bad, "'")) } msg } diff -Nru r-bioc-biobase-2.14.0/R/methods-aggregator.R r-bioc-biobase-2.20.0/R/methods-aggregator.R --- r-bioc-biobase-2.14.0/R/methods-aggregator.R 2011-10-31 23:31:56.000000000 +0000 +++ r-bioc-biobase-2.20.0/R/methods-aggregator.R 2013-04-03 22:22:27.000000000 +0000 @@ -18,11 +18,11 @@ if(is.character(x)) { for( i in 1:length(x) ) { nm <- x[i] - if( !exists(nm, env=aggenv(agg), inherits=FALSE) ) - assign(nm, env=aggenv(agg), initfun(agg)(nm, x)) + if( !exists(nm, envir=aggenv(agg), inherits=FALSE) ) + assign(nm, envir=aggenv(agg), initfun(agg)(nm, x)) else { - v1 <- get(nm, env=aggenv(agg)) - assign(nm, aggfun(agg)(nm, v1), env=aggenv(agg)) + v1 <- get(nm, envir=aggenv(agg)) + assign(nm, aggfun(agg)(nm, v1), envir=aggenv(agg)) } } } @@ -31,11 +31,11 @@ nms <- names(x) for( i in 1:length(x) ) { nm <- nms[i] - if( !exists(nm, env=aggenv(agg), inherits=FALSE) ) - assign(nm, env=aggenv(agg), initfun(agg)(nm, x[[i]])) + if( !exists(nm, envir=aggenv(agg), inherits=FALSE) ) + assign(nm, envir=aggenv(agg), initfun(agg)(nm, x[[i]])) else { - v1 <- get(nm, env=aggenv(agg)) - assign(nm, env=aggenv(agg), aggfun(agg)(nm, v1, x[[i]])) + v1 <- get(nm, envir=aggenv(agg)) + assign(nm, envir=aggenv(agg), aggfun(agg)(nm, v1, x[[i]])) } } } diff -Nru r-bioc-biobase-2.14.0/R/methods-annotatedDataset.R r-bioc-biobase-2.20.0/R/methods-annotatedDataset.R --- r-bioc-biobase-2.14.0/R/methods-annotatedDataset.R 2011-10-31 23:31:56.000000000 +0000 +++ r-bioc-biobase-2.20.0/R/methods-annotatedDataset.R 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -setMethod("initialize", "annotatedDataset", - function(.Object, ...) { - .Defunct(msg="The annotatedDataset class is defunct") - }) diff -Nru r-bioc-biobase-2.14.0/R/methods-container.R r-bioc-biobase-2.20.0/R/methods-container.R --- r-bioc-biobase-2.14.0/R/methods-container.R 2011-10-31 23:31:56.000000000 +0000 +++ r-bioc-biobase-2.20.0/R/methods-container.R 2013-04-03 22:22:27.000000000 +0000 @@ -22,8 +22,8 @@ cv <- class(value) cont <- content(x) if( !extends(cv, cont) ) - stop(paste("the container is class", cont, - "the object is class", cv, "cannot assign", sep=" ")) + stop("the container is class '", cont, + "' the object is class '", cv, "' cannot assign") x@x[[i]] <- value x } diff -Nru r-bioc-biobase-2.14.0/R/methods-data.frame.R r-bioc-biobase-2.20.0/R/methods-data.frame.R --- r-bioc-biobase-2.14.0/R/methods-data.frame.R 2011-10-31 23:31:56.000000000 +0000 +++ r-bioc-biobase-2.20.0/R/methods-data.frame.R 1970-01-01 00:00:00.000000000 +0000 @@ -1,105 +0,0 @@ -setMethod("combine", - signature(x="data.frame", y="data.frame"), - function(x, y, ...) { - if (all(dim(x)==0) && all(dim(y)==0)) - return(x) - else if (all(dim(x)==0)) return(y) - else if (all(dim(y)==0)) return(x) - - uniqueRows <- unique(c(row.names(x), row.names(y))) - uniqueCols <- unique(c(names(x), names(y))) - sharedCols <- intersect(names(x), names(y)) - - ## check possible to combine - alleq <- function(x, y) { - res <- all.equal(x, y, check.attributes=FALSE) - if (!is.logical(res)) { - warning(res) - FALSE - } else TRUE - } - sharedRows <- intersect(row.names(x), row.names(y)) - ok <- sapply(sharedCols, function(nm) { - if (!all(class(x[[nm]]) == class(y[[nm]]))) return(FALSE) - switch(class(x[[nm]])[[1]], - factor= { - if (!alleq(levels(x[[nm]]), levels(y[[nm]]))) { - warning("data frame column '", nm, - "' levels not all.equal", - call.=FALSE) - TRUE - } else if (!alleq(x[sharedRows, nm, drop=FALSE], - y[sharedRows, nm, drop=FALSE])) { - warning("data frame column '", nm, - "' shared rows not all equal", - call.=FALSE) - FALSE - } else TRUE - }, - ## ordered and non-factor columns need to - ## satisfy the following identity; it seems - ## possible that ordered could be treated - ## differently, but these have not been - ## encountered. - ordered=, - if (!alleq(x[sharedRows, nm, drop=FALSE], - y[sharedRows, nm, drop=FALSE])) { - warning("data frame column '", nm, - "' shared rows not all equal") - FALSE - } else TRUE) - }) - if (!all(ok)) - stop("data.frames contain conflicting data:", - "\n\tnon-conforming colname(s): ", paste(sharedCols[!ok], collapse=", ")) - - ## x or y with zero rows -- make palatable to merge, but drop before return - if (length(uniqueRows)==0) { - x <- x["tmp",,drop=FALSE] - y <- y["tmp",,drop=FALSE] - } else if (nrow(x)==0) { - x <- x[row.names(y),,drop=FALSE] - row.names(x) <- row.names(y) - } else if (nrow(y)==0) { - y <- y[row.names(x),,drop=FALSE] - row.names(y) <- row.names(x) - } - - ## make colnames of merged data robust - if (length(uniqueCols)>0) - extLength <- max(nchar(sub(".*\\.", "", uniqueCols)))+1 - else extLength <- 1 - extX <- paste(c(".", rep("x", extLength)), collapse="") - extY <- paste(c(".", rep("y", extLength)), collapse="") - z <- merge(x, y, by="row.names", all=TRUE, suffixes=c(extX,extY)) - - ## shared cols - for (nm in sharedCols) { - nmx <- paste(nm, extX, sep="") - nmy <- paste(nm, extY, sep="") - z[[nm]] <- - switch(class(z[[nmx]])[[1]], - AsIs= I(ifelse(is.na(z[[nmx]]), z[[nmy]], z[[nmx]])), - factor= { - col <- ifelse(is.na(z[[nmx]]), - as.character(z[[nmy]]), as.character(z[[nmx]])) - if (!identical(levels(z[[nmx]]), levels(z[[nmy]]))) - factor(col) - else factor(col, levels=levels(z[[nmx]])) - }, - { - col <- ifelse(is.na(z[[nmx]]), z[[nmy]], z[[nmx]]) - class(col) <- class(z[[nmx]]) - col - }) - } - - ## tidy - row.names(z) <- - if (is.integer(attr(x, "row.names")) && - is.integer(attr(y, "row.names"))) - as.integer(z$Row.names) - else z$Row.names - z$Row.names <- NULL - z[uniqueRows, uniqueCols, drop=FALSE] - }) diff -Nru r-bioc-biobase-2.14.0/R/methods-eSet.R r-bioc-biobase-2.20.0/R/methods-eSet.R --- r-bioc-biobase-2.14.0/R/methods-eSet.R 2011-10-31 23:31:56.000000000 +0000 +++ r-bioc-biobase-2.20.0/R/methods-eSet.R 2013-04-03 22:22:27.000000000 +0000 @@ -267,7 +267,8 @@ setMethod("show", signature=signature(object="eSet"), function(object) { - cat(class( object ), " (storageMode: ", storageMode(object), ")\n", sep="") + cat(class(object), " (storageMode: ", + storageMode(object), ")\n", sep="") adim <- dim(object) if (length(adim)>1) cat("assayData:", @@ -343,6 +344,16 @@ unsafeSetSlot(object, "assayData", ad) }) +setMethod("dimnames", "eSet", function(x) { + list(featureNames(x), sampleNames(x)) +}) + +setReplaceMethod("dimnames", "eSet", function(x, value) { + featureNames(x) <- value[[1]] + sampleNames(x) <- value[[2]] + x +}) + setMethod("dim", "eSet", function(x) assayDataDim(assayData(x))) setMethod("dims", "eSet", function(object) assayDataDims(assayData(object))) @@ -660,8 +671,8 @@ x="eSet", y="eSet"), function(x, y, ...) { if (class(x) != class(y)) - stop(paste("objects must be the same class, but are ", - class(x), ", ", class(y), sep="")) + stop("objects must be the same class, but are '", + class(x), "', '", class(y), "'") if (any(annotation(x) != annotation(y))) stop("objects have different annotations: ", annotation(x), ", ", annotation(y)) @@ -676,24 +687,3 @@ x }) -## -## Defunct methods -## - -setMethod("reporterNames", "eSet", function(object) { - .Defunct("featureNames", "Biobase") -}) -setReplaceMethod("reporterNames", c("eSet", "character"), function(object, value) { - .Defunct("featureNames<-", "Biobase") -}) - -setMethod("eList", "eSet", function(object) { - .Defunct("assayData", "Biobase") -}) -setReplaceMethod("eList", c("eSet", "AssayData"), function(object, value) { - .Defunct("assayData<-", "Biobase") -}) - -setMethod("getExpData", c("eSet", "character"), function(object, name) { - .Defunct("assayData", "Biobase") -}) diff -Nru r-bioc-biobase-2.14.0/R/methods-exprSet.R r-bioc-biobase-2.20.0/R/methods-exprSet.R --- r-bioc-biobase-2.14.0/R/methods-exprSet.R 2011-10-31 23:31:56.000000000 +0000 +++ r-bioc-biobase-2.20.0/R/methods-exprSet.R 1970-01-01 00:00:00.000000000 +0000 @@ -1,9 +0,0 @@ -setMethod("initialize", "exprSet", - function(.Object, ...) { - .Defunct(msg="The exprSet class is defunct, use ExpressionSet instead") - }) - -read.exprSet <- function(exprs, se.exprs, phenoData, annotation, - description, notes, seps = "\t" ) { - .Defunct("readExpressionSet", "Biobase") -} diff -Nru r-bioc-biobase-2.14.0/R/methods-matrix.R r-bioc-biobase-2.20.0/R/methods-matrix.R --- r-bioc-biobase-2.14.0/R/methods-matrix.R 2011-10-31 23:31:56.000000000 +0000 +++ r-bioc-biobase-2.20.0/R/methods-matrix.R 1970-01-01 00:00:00.000000000 +0000 @@ -1,32 +0,0 @@ -setMethod("combine", c("matrix", "matrix"), function(x, y, ...) { - if (length(y)==0) - return(x) - else if (length(x)==0) - return(y) - if (mode(x) != mode(y)) - stop("matrix modes ", mode(x), ", ", mode(y), " differ") - if (typeof(x) != typeof(y)) - warning("matrix typeof ", typeof(x), ", ", typeof(y), - " differ") - xdim <- dimnames(x) - ydim <- dimnames(y) - if (is.null(xdim) || is.null(ydim) || - any(sapply(xdim, is.null)) || - any(sapply(ydim, is.null))) - stop("matricies must have dimnames for 'combine'") - sharedRows <- intersect(xdim[[1]], ydim[[1]]) - sharedCols <- intersect(xdim[[2]], ydim[[2]]) - ok <- all.equal(x[sharedRows, sharedCols], y[sharedRows, sharedCols]) - if (!isTRUE(ok)) - stop("matrix shared row and column elements differ: ", - ok) - unionRows <- union(xdim[[1]], ydim[[1]]) - unionCols <- union(xdim[[2]], ydim[[2]]) - - m <- matrix(new(class(as.vector(x))), - nrow=length(unionRows), ncol=length(unionCols), - dimnames=list(unionRows, unionCols)) - m[rownames(x), colnames(x)] <- x - m[rownames(y), colnames(y)] <- y - m -}) diff -Nru r-bioc-biobase-2.14.0/R/methods-phenoData.R r-bioc-biobase-2.20.0/R/methods-phenoData.R --- r-bioc-biobase-2.14.0/R/methods-phenoData.R 2011-10-31 23:31:56.000000000 +0000 +++ r-bioc-biobase-2.20.0/R/methods-phenoData.R 1970-01-01 00:00:00.000000000 +0000 @@ -1,18 +0,0 @@ -setMethod("initialize", "phenoData", - function(.Object, ...) { - .Defunct(msg="The phenoData class is defunct, use AnnotatedDataFrame (with ExpressionSet) instead") - }) - -df2pD <- function(x, varLabels, varMetadata) { - .Defunct() -} - -read.pD <- function(filename = NULL, ...) { - .Defunct() -} - -read.phenoData <- function(filename = NULL, sampleNames = NULL, - widget = getOption("BioC")$Base$use.widgets,...) { - - .Defunct(msg="read.phenoData is defunct, use read.AnnotatedDataFrame instead") -} diff -Nru r-bioc-biobase-2.14.0/R/packages.R r-bioc-biobase-2.20.0/R/packages.R --- r-bioc-biobase-2.14.0/R/packages.R 2011-10-31 23:31:56.000000000 +0000 +++ r-bioc-biobase-2.20.0/R/packages.R 2013-04-03 22:22:27.000000000 +0000 @@ -10,11 +10,11 @@ ## check arguments for (a in c("pkgname", "destinationDir", "originDir")) if (!is.character(get(a)) || length(get(a))!=1) - stop(paste("'", a, "' must be a character vector of length 1.", sep="")) + stop("'", a, "' must be character(1)") ## check whether destinationDir, originDir exist and are directories for (a in c("destinationDir", "originDir")) if(!file.exists(get(a)) || !file.info(get(a))$isdir) - stop(paste("'", a, "' must be a directory (", get(a), ")\n.", sep="")) + stop("'", a, "' must be a directory (", get(a), ")") ## locate / remove / create destination directory pkgdir = file.path(destinationDir, pkgname) if (!quiet) @@ -23,17 +23,17 @@ if (unlink) { unlink(pkgdir, recursive=TRUE) if (file.exists(pkgdir)) { - stop(paste("Directory", pkgdir, "exists and could not be removed.", - "Please remove it manually or choose another destination directory.")) + stop("directory '", pkgdir, "' exists and could not be removed; ", + "remove it manually or choose another destination directory") } else { if(!quiet) - cat(paste("Existing", pkgdir, "was removed.\n")) + cat("existing", pkgdir, "was removed.\n") } } else - stop(paste("Directory", pkgdir, "exists. Please use unlink=TRUE to remove it", - "or choose another destination directory.")) + stop("directory '", pkgdir, "' exists; use unlink=TRUE ", + "to remove it, or choose another destination directory") } ## if (file.exists) ## predefined symbols symbolValues = append(symbolValues, list(TODAY=date(), PKGNAME=pkgname)) @@ -48,13 +48,13 @@ options(warn=-1) desc <- packageDescription(pkg, lib.loc, "Version") if (is.na(desc)) - stop(paste("Package",pkg,"does not exist")) + stop("package '", pkg, "' does not exist") desc } # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - dumpPackTxt <- function (package) { # stolen from "library" to get descriptive info out on stdout - pkgpath <- .find.package(package) + pkgpath <- find.package(package) # outFile <- tempfile("Rlibrary") # outConn <- file(outFile, open = "w") docFiles <- file.path(pkgpath, c("TITLE", "DESCRIPTION", "INDEX")) @@ -82,8 +82,8 @@ vMD = varMetadata(pD) vL = varLabels(pD) for(i in 1:length(vL) ) { - item = paste("\\item \\code{", vL[i], "}: ", vMD[i,1], sep="") + item = paste0("\\item \\code{", vL[i], "}: ", vMD[i,1]) covs = paste(covs, item, sep="\n") } - paste(fmt, covs, "\n}\n}\n", sep="") + paste0(fmt, covs, "\n}\n}\n") } diff -Nru r-bioc-biobase-2.14.0/R/strings.R r-bioc-biobase-2.20.0/R/strings.R --- r-bioc-biobase-2.14.0/R/strings.R 2011-10-31 23:31:56.000000000 +0000 +++ r-bioc-biobase-2.20.0/R/strings.R 2013-04-03 22:22:27.000000000 +0000 @@ -11,7 +11,7 @@ if(is.na(exdent) || exdent>width) stop("invalid argument 'exdent'") ww <- width-exdent - lb <- paste(collapse, paste(rep(" ", exdent), collapse=""), sep="") + lb <- paste0(collapse, paste(rep(" ", exdent), collapse="")) rv <- character(length(x)) for(i in seq(along=x)) { first <- 1 diff -Nru r-bioc-biobase-2.14.0/R/tools.R r-bioc-biobase-2.20.0/R/tools.R --- r-bioc-biobase-2.14.0/R/tools.R 2011-10-31 23:31:56.000000000 +0000 +++ r-bioc-biobase-2.20.0/R/tools.R 2013-04-03 22:22:27.000000000 +0000 @@ -25,7 +25,7 @@ if (is.null(bioCoption)) bioCoption <- "http://www.bioconductor.org" ## Now check to see if we can connect to the BioC website - biocURL <- url(paste(bioCoption,"/main.html",sep="")) + biocURL <- url(paste0(bioCoption,"/main.html")) options(show.error.messages=FALSE) test <- try(readLines(biocURL)[1]) options(show.error.messages=TRUE) @@ -99,13 +99,14 @@ } ## check for unresolved symbols if(!allowUnresolvedSymbols) { - re = regexpr(paste(symbolDelimiter, ".+", symbolDelimiter, sep=""), txt) + re = regexpr(paste0(symbolDelimiter, ".+", symbolDelimiter), txt) wh = which(re>0) if(length(wh)>0) { ml = attr(re, "match.length") mess = "UNRESOLVED SYMBOLS:\n" - mess = paste(mess, paste(sapply(wh, function(i) - paste("Line", i, ":", substr(txt[i], re[i], re[i] + ml[i]))), collapse="\n"), sep="") + mess <- paste0(mess, paste(sapply(wh, function(i) { + paste("Line", i, ":", substr(txt[i], re[i], re[i] + ml[i])) + }), collapse="\n")) stop(mess) } } @@ -150,7 +151,7 @@ ## if 'dest' does not exist, create if (file.access(dest) != 0) { if (!dir.create(dest)) - stop(paste("'dest' does not exist, and it cannot be created:", dest)) + stop("'dest' does not exist, and cannot be created: ", dest) } ## process src isdir = file.info(src)$isdir @@ -162,7 +163,7 @@ destname = file.path(dest, tmp) if (isdir[k]) { if(!dir.create(destname)) - stop(paste("directory cannot be created:", destname)) + stop("directory cannot be created: ", destname) cpSubs(dir(src[k], full.names=TRUE), destname) } else @@ -174,7 +175,7 @@ stop(usage) } ## cpSubs ## DO IT! - nm = paste(symbolDelimiter, names(symbolValues), symbolDelimiter, sep="") + nm = paste0(symbolDelimiter, names(symbolValues), symbolDelimiter) cpSubs(src, dest) } # ========================================================================== @@ -245,7 +246,7 @@ } name <- as.character(pexpr[[2]]) RHS <- pexpr[[3]] - cachefile <- file.path(dir, paste(prefix, name, ".RData", sep="")) + cachefile <- file.path(dir, paste0(prefix, name, ".RData")) if(file.exists(cachefile)) { load(cachefile) assign(name, get(name), envir=parent.frame()) @@ -257,23 +258,6 @@ invisible(get(name, envir=parent.frame())) } ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -getObjectSlots <- function(object) { # object, rather than class defn, slots - if(!is.object(object) || isVirtualClass(class(object))) - return(NULL) - value <- attributes(object) - value$class <- NULL - if(is(object, "vector")) { - .Data <- as.vector(object) - attr(.Data, "class") <- NULL - attrNames <- c('comment', 'dim', 'dimnames', 'names', 'row.names', 'tsp') - for (nm in names(value)[names(value) %in% attrNames]) - attr(.Data, nm) <- value[[nm]] - value <- value[!names(value) %in% attrNames] - value$.Data <- .Data - } - value -} - validMsg <- function(msg, result) { if (is.character(result)) { append(msg, result) @@ -296,9 +280,8 @@ ## repeats until it gets allowable input if(interactive()){ repeat { - allowMsg <- paste("[",paste(allowed,collapse="/"), - "] ", sep="") - outMsg <- paste(msg,allowMsg) + allowMsg <- paste0("[", paste(allowed,collapse="/"), "] ") + outMsg <- paste(msg, allowMsg) cat(outMsg) if(case.sensitive) ans <- readLines(n=1) @@ -307,7 +290,7 @@ if (ans %in% allowed) break else - cat(paste(ans,"is not a valid response, try again.\n")) + cat(ans, "is not a valid response, try again.\n") } return(ans) }else{ diff -Nru r-bioc-biobase-2.14.0/R/updateObject.R r-bioc-biobase-2.20.0/R/updateObject.R --- r-bioc-biobase-2.14.0/R/updateObject.R 2011-10-31 23:31:56.000000000 +0000 +++ r-bioc-biobase-2.20.0/R/updateObject.R 1970-01-01 00:00:00.000000000 +0000 @@ -1,110 +0,0 @@ -setMethod("updateObject", signature(object="ANY"), - function(object, ..., verbose=FALSE) { - if (verbose) - message("updateObject(object = 'ANY') default for object of class '", class(object), "'") - if (length(getObjectSlots(object)) > 0 && - !any(class(object) %in% c("data.frame"))) { - updateObjectFromSlots(object, ..., verbose=verbose) - } else object - }) - -setMethod("updateObject", signature(object="list"), - function(object, ..., verbose=FALSE) { - if (verbose) message("updateObject(object = 'list')") - if ("class" %in% names(attributes(object))) callNextMethod() # old-style S4 - else { - result <- lapply(object, updateObject, ..., verbose=verbose) - attributes(result) <- attributes(object) - result - } - }) - -setMethod("updateObject", signature(object="environment"), - function(object, ..., verbose=FALSE) { - if (verbose) message("updateObject(object = 'environment')") - envLocked <- environmentIsLocked(object) - if (verbose) { - if (envLocked) - warning("updateObject duplicating locked environment") - else - warning("updateObject modifying environment") - } - env <- - if (envLocked) new.env() - else object - lapply(ls(object, all=TRUE), - function(elt) { # side-effect! - bindingLocked <- bindingIsLocked(elt, object) - if (!envLocked && bindingLocked) - stop("updateObject object = 'environment' ", - "cannot modify locked binding '", elt, "'") - else { - env[[elt]] <<- updateObject(object[[elt]], ..., verbose=verbose) - if (bindingLocked) lockBinding(elt, env) - } - NULL - }) - attributes(env) <- attributes(object) - if (envLocked) - lockEnvironment(env) - env - }) - -updateObjectFromSlots <- function(object, objclass = class(object), ..., verbose=FALSE) { - if (is(object, "environment")) { - if (verbose) message("returning original object of class 'environment'") - return(object) - } - classSlots <- slotNames(objclass) - if (is.null(classSlots)) { - if (verbose) message("definition of '", objclass, "' has no slots; ", - "returning original object") - return(object) - } - errf <- function(...) - function(err) { - if (verbose) - message(..., ":\n ", conditionMessage(err), - "\n trying next method...") - NULL - } - if (verbose) message("updateObjectFromSlots(object = '", class(object), - "' class = '", objclass, "')") - objectSlots <- getObjectSlots(object) - ## de-mangle and remove NULL - nulls <- sapply(names(objectSlots), function(slt) is.null(slot(object, slt))) - objectSlots[nulls] <- NULL - joint <- intersect(names(objectSlots), classSlots) - toUpdate <- joint[joint!=".Data"] - objectSlots[toUpdate] <- lapply(objectSlots[toUpdate], updateObject, ..., verbose=verbose) - toDrop <- which(!names(objectSlots) %in% classSlots) - if (length(toDrop) > 0) { - warning("dropping slot(s) ", - paste(names(objectSlots)[toDrop],collapse=", "), - " from object = '", class(object), "'") - objectSlots <- objectSlots[-toDrop] - } - ## ad-hoc methods for creating new instances - res <- NULL - if (is.null(res)) { - if (verbose) message("heuristic updateObjectFromSlots, method 1") - res <- - tryCatch({ - do.call(new, c(objclass, objectSlots[joint])) - }, error=errf("'new(\"", objclass, "\", ...)' from slots failed")) - } - if (is.null(res)) { - if (verbose) message("heuristic updateObjectFromSlots, method 2") - res <- - tryCatch({ - obj <- do.call(new, list(objclass)) - for (slt in joint) slot(obj, slt) <- updateObject(objectSlots[[slt]], ..., verbose=verbose) - obj - }, error=errf("failed to add slots to 'new(\"", objclass, "\", ...)'")) - } - if (is.null(res)) - stop("could not updateObject to class '", objclass, "'", - "\nconsider defining an 'updateObject' method for class '", - class(object), "'") - res -} diff -Nru r-bioc-biobase-2.14.0/R/vignettes.R r-bioc-biobase-2.20.0/R/vignettes.R --- r-bioc-biobase-2.14.0/R/vignettes.R 2011-10-31 23:31:56.000000000 +0000 +++ r-bioc-biobase-2.20.0/R/vignettes.R 2013-04-03 22:22:27.000000000 +0000 @@ -9,12 +9,15 @@ stop("`package' must be a character vector of package names") rows <- match(package, pkgs) if( all(is.na(rows)) ) - stop("packages: ", paste(package,collapse=", "), " are not loaded") + stop("packages '", paste(package, collapse="', '"), + "' are not loaded") if( any(is.na(rows)) ) - warning("packages ", paste(package[is.na(rows)], collapse=", "), " are not loaded") + warning("packages '", + paste(package[is.na(rows)], collapse="', '"), + "' are not loaded") pkgs <- pkgs[rows[!is.na(rows)]] } - vigrds = file.path(.find.package(pkgs), "Meta", "vignette.rds") + vigrds = file.path(find.package(pkgs), "Meta", "vignette.rds") ## construct data frame with: package, path, title pkgVigs = vector(mode="list", length=length(vigrds)) @@ -40,10 +43,14 @@ # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - openVignette = function(package=NULL) { vig = getPkgVigs(package) - if(is.null(vig)) { - warning(paste(sep="", "No vignettes found", - ifelse(is.null(package), ".\n", sprintf(" for package%s %s.\n", - ifelse(length(package)==1, "", "s"), paste(package, collapse=", "))))) + if (is.null(vig)) { + txt <- "" + if (!is.null(package)) { + ss <- if (length(package)==1) "" else "s" + pkgs <- paste(package, collapse=", ") + txt <- sprintf(" for package%s %s", ss, pkgs) + } + warning("no vignettes found", txt) } else { hasnofile = is.na(vig$filename) vig$title[hasnofile] = paste(vig$title[hasnofile], "[-]") @@ -61,7 +68,7 @@ if(!is.na(vif)) { openPDF(vif) cat("Opening", vif, "\n") - ## browseURL(paste("file://", vig[index],sep="")) + ## browseURL(paste0("file://", vig[index])) } else { stop("Sorry, no PDF file could be found for this vignette.\n", "Please reinstall the package with built vignettes.") @@ -83,7 +90,7 @@ warning(sprintf("%s contains no vignette, nothing is added to the menu bar", pkgName)) } else { vigMtrx = readRDS(vigFile) - vigs = file.path(.find.package(pkgName), "doc", vigMtrx[, "PDF"]) + vigs = file.path(find.package(pkgName), "doc", vigMtrx[, "PDF"]) names(vigs) = vigMtrx[,"Title"] if (!"Vignettes" %in% winMenuNames()) @@ -94,7 +101,7 @@ for (i in seq(along=vigs)) winMenuAddItem(pkgMenu, names(vigs)[i], - paste("shell.exec(\"", vigs[i], "\")", sep="")) + paste0("shell.exec(\"", vigs[i], "\")")) } ## else ans = TRUE diff -Nru r-bioc-biobase-2.14.0/R/zzz.R r-bioc-biobase-2.20.0/R/zzz.R --- r-bioc-biobase-2.14.0/R/zzz.R 2011-10-31 23:31:56.000000000 +0000 +++ r-bioc-biobase-2.20.0/R/zzz.R 2013-04-03 22:22:27.000000000 +0000 @@ -8,12 +8,14 @@ } .onAttach <- function(libname, pkgname) { - packageStartupMessage( - paste("\nWelcome to Bioconductor\n", - "Vignettes contain introductory material. To view, type", - "'browseVignettes()'. To cite Bioconductor, see", - "'citation(\"Biobase\")' and for packages 'citation(\"pkgname\")'.\n", sep="\n ")) - addVigs2WinMenu("Biobase") + msg0 <- "Vignettes contain introductory material; view with + 'browseVignettes()'. To cite Bioconductor, see + 'citation(\"Biobase\")', and for packages + 'citation(\"pkgname\")'." + msg <- strwrap(paste(msg0, collapse=""), exdent=4, indent=4) + packageStartupMessage(paste(c("Welcome to Bioconductor\n", msg), + collapse="\n"), "\n") + addVigs2WinMenu("Biobase") } .onUnload <- function( libpath ) { Binary files /tmp/23r_lGFEta/r-bioc-biobase-2.14.0/data/SW.rda and /tmp/OxmT1wIVc2/r-bioc-biobase-2.20.0/data/SW.rda differ Binary files /tmp/23r_lGFEta/r-bioc-biobase-2.14.0/data/sample.ExpressionSet.rda and /tmp/OxmT1wIVc2/r-bioc-biobase-2.20.0/data/sample.ExpressionSet.rda differ Binary files /tmp/23r_lGFEta/r-bioc-biobase-2.14.0/data/sample.MultiSet.rda and /tmp/OxmT1wIVc2/r-bioc-biobase-2.20.0/data/sample.MultiSet.rda differ Binary files /tmp/23r_lGFEta/r-bioc-biobase-2.14.0/data/seD.rda and /tmp/OxmT1wIVc2/r-bioc-biobase-2.20.0/data/seD.rda differ diff -Nru r-bioc-biobase-2.14.0/debian/changelog r-bioc-biobase-2.20.0/debian/changelog --- r-bioc-biobase-2.14.0/debian/changelog 2013-05-05 02:36:29.000000000 +0000 +++ r-bioc-biobase-2.20.0/debian/changelog 2013-05-05 02:36:30.000000000 +0000 @@ -1,3 +1,28 @@ +r-bioc-biobase (2.20.0-1precise0) precise; urgency=low + + * Compilation for Ubuntu 12.04.2 LTS + + -- Michael Rutter Sun, 05 May 2013 02:24:26 +0000 + +r-bioc-biobase (2.20.0-1) unstable; urgency=low + + [ Andreas Tille ] + 910457e debian/upstream: Added citations + + [ Charles Plessy ] + 910457e Imported Upstream version 2.20.0 + d1f8572 No new copyright nor license notice in the new upstream versions. + 4a880aa Using Debhelper 9 + 6861f53 Conforms with Policy version 3.9.4. + 4a49c97 Normalised Debian copyright file with 'cme fix dpkg-copyright'. + 4ce8c62 Removed obsolete field DM-Upload-Allowed. + 64b2da7 Normalised debian/control with 'cme fix dpkg-control'. + c5c1206 Repaired Debian watch file. + d8c85b8 Normalised VCS URLs following Lintian's standard. + 4a6818a Depend on r-bioc-biocgenerics (>= 0.3.2). + + -- Charles Plessy Mon, 08 Apr 2013 13:00:55 +0900 + r-bioc-biobase (2.14.0-1) unstable; urgency=low [cb6b786] Bioconductor release 2.9. diff -Nru r-bioc-biobase-2.14.0/debian/compat r-bioc-biobase-2.20.0/debian/compat --- r-bioc-biobase-2.14.0/debian/compat 2013-05-05 02:36:29.000000000 +0000 +++ r-bioc-biobase-2.20.0/debian/compat 2013-05-05 02:36:30.000000000 +0000 @@ -1 +1 @@ -8 +9 diff -Nru r-bioc-biobase-2.14.0/debian/control r-bioc-biobase-2.20.0/debian/control --- r-bioc-biobase-2.14.0/debian/control 2013-05-05 02:36:29.000000000 +0000 +++ r-bioc-biobase-2.20.0/debian/control 2013-05-05 02:36:30.000000000 +0000 @@ -1,20 +1,23 @@ Source: r-bioc-biobase -Section: gnu-r -Priority: optional Maintainer: Debian Med Packaging Team -DM-Upload-Allowed: yes Uploaders: Charles Plessy -Build-Depends: cdbs, debhelper (>= 8), r-base-dev (>= 2.10) -Standards-Version: 3.9.2 -Vcs-Browser: http://git.debian.org/?p=debian-med/r-bioc-biobase.git -Vcs-Git: git://git.debian.org/git/debian-med/r-bioc-biobase.git +Section: gnu-r +Priority: optional +Build-Depends: cdbs, + debhelper (>= 9), + r-base-dev, + r-bioc-biocgenerics (>= 0.3.2) +Standards-Version: 3.9.4 +Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-med/r-bioc-biobase.git +Vcs-Git: git://anonscm.debian.org/debian-med/r-bioc-biobase.git Homepage: http://www.bioconductor.org Package: r-bioc-biobase Architecture: any -# Keep until Ubuntu LTS 12.4 -Pre-Depends: dpkg (>= 1.15.6) -Depends: ${shlibs:Depends}, ${misc:Depends}, ${R:Depends} +Depends: ${shlibs:Depends}, + ${misc:Depends}, + ${R:Depends}, + r-bioc-biocgenerics (>= 0.3.2) Description: base functions for Bioconductor Biobase is part of the Bioconductor project, and is used by many other packages. Biobase contains standardized data structures to represent genomic @@ -31,3 +34,4 @@ packages provides in its Debian documentation instructions on how to install unofficial auto-generated Bioconductor packages for Debian and Ubuntu systems, that are prepared by members of the Debian Med team. + diff -Nru r-bioc-biobase-2.14.0/debian/copyright r-bioc-biobase-2.20.0/debian/copyright --- r-bioc-biobase-2.14.0/debian/copyright 2013-05-05 02:36:29.000000000 +0000 +++ r-bioc-biobase-2.20.0/debian/copyright 2013-05-05 02:36:30.000000000 +0000 @@ -1,24 +1,21 @@ -Format: http://dep.debian.net/deps/dep5/ -Source: http://www.bioconductor.org/packages/2.9/bioc/src/contrib/Biobase_2.14.0.tar.gz +Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Source: http://bioconductor.org/packages/2.12/bioc/src/contrib/Biobase_2.20.0.tar.gz Files: * Copyright: none claimed, but an author list is provided in the DESCRIPTION file. License: Artistic-2.0 - Files: src/rowMedians.c src/anyMissing.c Copyright: © Henrik Bengtsson, 2007 License: Artistic-2.0 Comment: Copies from the CRAN matrixStats packages, see: http://cran.r-project.org/web/packages/matrixStats - Files: src/envir.c Copyright: © R. Gentleman, 2003 License: Artistic-2.0 Comment: R. Gentleman is listed as author in the DESCRIPTION file. - Files: debian/* Copyright: © 2011, Charles Plessy License: BOLA-1.1 @@ -44,7 +41,6 @@ to replace them. 6. Be tolerant. Everything that's good in nature comes from cooperation. - License: Artistic-2.0 Copyright (c) 2000-2006, The Perl Foundation. . diff -Nru r-bioc-biobase-2.14.0/debian/upstream r-bioc-biobase-2.20.0/debian/upstream --- r-bioc-biobase-2.14.0/debian/upstream 1970-01-01 00:00:00.000000000 +0000 +++ r-bioc-biobase-2.20.0/debian/upstream 2013-05-05 02:36:30.000000000 +0000 @@ -0,0 +1,12 @@ +Reference: + Author: Robert C Gentleman and Vincent J Carey and Douglas M Bates and Ben Bolstad and Marcel Dettling and Sandrine Dudoit and Byron Ellis and Laurent Gautier and Yongchao Ge and Jeff Gentry and Kurt Hornik and Torsten Hothorn and Wolfgang Huber and Stefano Iacus and Rafael Irizarry and Friedrich Leisch and Cheng Li and Martin Maechler and Anthony J Rossini and Gunther Sawitzki and Colin Smith and Gordon Smyth and Luke Tierney and Jean Y H Yang and Jianhua Zhang + Title: "Bioconductor: Open software development for computational biology and bioinformatics" + Journal: Genome Biology + Year: 2004 + Volume: 5 + Number: 10 + Pages: R80 + DOI: 10.1186/gb-2004-5-10-r80 + PMID: 15461798 + URL: http://genomebiology.com/2004/5/10/R80 + eprint: http://genomebiology.com/content/pdf/gb-2004-5-10-r80.pdf diff -Nru r-bioc-biobase-2.14.0/debian/watch r-bioc-biobase-2.20.0/debian/watch --- r-bioc-biobase-2.14.0/debian/watch 2013-05-05 02:36:29.000000000 +0000 +++ r-bioc-biobase-2.20.0/debian/watch 2013-05-05 02:36:30.000000000 +0000 @@ -1,5 +1,4 @@ version=3 # This tracks the current stable version of bioconductor -http://www.bioconductor.org/help/bioc-views/release/bioc/html/Biobase.html \ - /packages/.*/bioc/src/contrib/Biobase_(.*).tar.gz +http://bioconductor.org/packages/release/bioc/html/Biobase.html .*/Biobase_(.*).tar.gz diff -Nru r-bioc-biobase-2.14.0/inst/UnitTests/AnnotatedDataFrame_test.R r-bioc-biobase-2.20.0/inst/UnitTests/AnnotatedDataFrame_test.R --- r-bioc-biobase-2.14.0/inst/UnitTests/AnnotatedDataFrame_test.R 2011-10-31 23:32:00.000000000 +0000 +++ r-bioc-biobase-2.20.0/inst/UnitTests/AnnotatedDataFrame_test.R 2013-04-03 22:22:34.000000000 +0000 @@ -38,10 +38,12 @@ checkVarMetadata(varMetadata(obj1), varMetadata(obj2), varMetadata(obj)) } checkUnchangedPData <- function(p1, p2, p) { - checkTrue(all(sapply(colnames(p1), - function(nm) identical(p[1:dim(p1)[[1]],nm], p1[,nm])))) - checkTrue(all(sapply(colnames(p2), - function(nm) identical(p[dim(p1)[[1]] + 1:dim(p1)[[1]],nm], p2[,nm])))) + checkTrue(all(sapply(colnames(p1), function(nm) { + identical(p[1:dim(p1)[[1]],nm], p1[,nm]) + }))) + checkTrue(all(sapply(colnames(p2), function(nm) { + identical(p[dim(p1)[[1]] + 1:dim(p1)[[1]],nm], p2[,nm]) + }))) } testEmptyCombine <- function() { @@ -108,6 +110,11 @@ obj2 <- obj1 varMetadata(obj2) <- varMetadata(obj1) checkTrue(identical(obj1, obj2)) + + to <- AnnotatedDataFrame(data.frame(Sample=1:5)) + df <- data.frame(labelDescription="foo", row.names="Sample") + varMetadata(to) <- df + checkTrue(validObject(to)) } testMetadataFactors <- function() { @@ -237,11 +244,6 @@ data=df, varMetadata=metaData) checkTrue(validObject(obj)) checkTrue(all(row.names(varMetadata(obj))==names(pData(obj)))) - ## build up piece-wise - obj <- new("AnnotatedDataFrame") - pData(obj) <- df - varMetadata(obj) <- metaData - checkTrue(validObject(obj)) } testAnnotatedDataFrameFrom <- function() { diff -Nru r-bioc-biobase-2.14.0/inst/UnitTests/AssayData_test.R r-bioc-biobase-2.20.0/inst/UnitTests/AssayData_test.R --- r-bioc-biobase-2.14.0/inst/UnitTests/AssayData_test.R 2011-10-31 23:32:00.000000000 +0000 +++ r-bioc-biobase-2.20.0/inst/UnitTests/AssayData_test.R 2013-04-03 22:22:34.000000000 +0000 @@ -37,6 +37,15 @@ } } +testAssayDataNew_named_dims <- function() +{ + nms0 <- list(letters[1:5], LETTERS[1:2]) + nms <- Map(setNames, nms0, nms0) + exprs <- matrix(0, nrow=5, ncol=2, dimnames=nms) + checkIdentical(nms0[[1]], featureNames(assayDataNew(exprs=exprs))) + checkIdentical(nms0[[2]], sampleNames(assayDataNew(exprs=exprs))) +} + testAssayDataCombine <- function() { checkAssayDataCombine(5,3) checkAssayDataCombine(0,0) diff -Nru r-bioc-biobase-2.14.0/inst/UnitTests/DataClasses_test.R r-bioc-biobase-2.20.0/inst/UnitTests/DataClasses_test.R --- r-bioc-biobase-2.14.0/inst/UnitTests/DataClasses_test.R 2011-10-31 23:32:00.000000000 +0000 +++ r-bioc-biobase-2.20.0/inst/UnitTests/DataClasses_test.R 2013-04-03 22:22:34.000000000 +0000 @@ -3,8 +3,7 @@ nms <- ls(getNamespace("Biobase"),all=TRUE) classes <- gsub(".__C__", "", nms[grep(".__C__", nms)]) isVirtual <- sapply(classes, function(nm) getClass(nm)@virtual) - isDefunct <- classes %in% c("exprSet", "phenoData") - res <- lapply(classes[!isVirtual & !isDefunct], + res <- lapply(classes[!isVirtual], function(x) suppressWarnings(new(x))) } diff -Nru r-bioc-biobase-2.14.0/inst/UnitTests/EsetSubclasses_test.R r-bioc-biobase-2.20.0/inst/UnitTests/EsetSubclasses_test.R --- r-bioc-biobase-2.14.0/inst/UnitTests/EsetSubclasses_test.R 2011-10-31 23:32:00.000000000 +0000 +++ r-bioc-biobase-2.20.0/inst/UnitTests/EsetSubclasses_test.R 2013-04-03 22:22:34.000000000 +0000 @@ -421,7 +421,8 @@ opts <- options() options(warn=-1) ## would like to be able to specify storage.mode, but how to specify?... - fp <- file.path("VersionedClass_data", "devel", "exprSet.Rda") + fp <- system.file(package="Biobase", "UnitTests", + "VersionedClass_data", "devel", "exprSet.Rda") load(fp) suppressMessages(e <- as(exprSet,"ExpressionSet")) checkNewAndOld(e,exprSet) @@ -433,7 +434,8 @@ pubMedIds(gm) = "10521349" checkNewGolubMerge(gm,Golub_Merge) - fp <- file.path("VersionedClass_data", "devel", "sample.eSet.rda") + fp <- system.file(package="Biobase", "UnitTests", + "VersionedClass_data", "devel", "sample.eSet.rda") load(fp) suppressMessages(es <- updateOldESet(sample.eSet, "SwirlSet")) checkNewSampleEset(es, sample.eSet) diff -Nru r-bioc-biobase-2.14.0/inst/UnitTests/NChannelSet_test.R r-bioc-biobase-2.20.0/inst/UnitTests/NChannelSet_test.R --- r-bioc-biobase-2.14.0/inst/UnitTests/NChannelSet_test.R 2011-10-31 23:32:00.000000000 +0000 +++ r-bioc-biobase-2.20.0/inst/UnitTests/NChannelSet_test.R 2013-04-03 22:22:34.000000000 +0000 @@ -211,11 +211,11 @@ c("R", "G", "_ALL_"))))) robj <- channel(obj, "R") checkTrue(validObject(robj)) - checkTrue(all(colnames(robj) %in% c("r", "both"))) + checkTrue(all(varLabels(robj) %in% c("r", "both"))) checkIdentical(assayDataElementNames(robj), "exprs") gobj <- channel(obj, "G") checkTrue(validObject(gobj)) - checkTrue(all(colnames(gobj) %in% c("g", "both"))) + checkTrue(all(varLabels(gobj) %in% c("g", "both"))) checkIdentical(assayDataElementNames(gobj), "exprs") } diff -Nru r-bioc-biobase-2.14.0/inst/UnitTests/UpdateObject_test.R r-bioc-biobase-2.20.0/inst/UnitTests/UpdateObject_test.R --- r-bioc-biobase-2.14.0/inst/UnitTests/UpdateObject_test.R 2011-10-31 23:32:00.000000000 +0000 +++ r-bioc-biobase-2.20.0/inst/UnitTests/UpdateObject_test.R 2013-04-03 22:22:34.000000000 +0000 @@ -1,90 +1,17 @@ -testUpdateObjectList <- function() { - setClass("A", - representation(x="numeric"), prototype(x=1:10), - where=.GlobalEnv) - a <- new("A") - l <- list(a,a) - checkTrue(identical(l, updateObject(l))) - - setMethod("updateObject", "A", - function(object, ..., verbose=FALSE) { - if (verbose) message("updateObject object = 'A'") - object@x <- -object@x - object - }, - where=.GlobalEnv) - - obj <- updateObject(l) - checkTrue(identical(lapply(l, function(elt) { elt@x <- -elt@x; elt }), - obj)) - removeMethod("updateObject", "A", where=.GlobalEnv) - removeClass("A", where=.GlobalEnv) -} - -testUpdateObjectEnv <- function() { - opts <- options() - options(warn=-1) - e <- new.env() - e$x=1 - e$.x=1 - obj <- updateObject(e) - checkTrue(identical(e,obj)) # modifies environment - - lockEnvironment(e) - obj <- updateObject(e) # copies environment - checkTrue(identical(lapply(ls(e, all=TRUE), function(x) x), - lapply(ls(obj, all=TRUE), function(x) x))) - checkTrue(!identical(e, obj)) # different environments - - e <- new.env() - e$x=1 - e$.x=1 - lockBinding("x", e) - checkException(updateObject(e), silent=TRUE) - - lockEnvironment(e) - obj <- updateObject(e) - checkTrue(TRUE==bindingIsLocked("x", obj)) # R bug, 14 May, 2006, fixed - checkTrue(FALSE==bindingIsLocked(".x", obj)) - options(opts) -} - -testUpdateObjectDefaults <- function() { +testUpdateObjectToDefaults <- function() { x <- 1:10 - checkTrue(identical(x, updateObject(x))) checkTrue(identical(1:10, updateObjectTo(x, 10:1))) x <- as.numeric(1:10) checkTrue(identical(as.integer(1:10), updateObjectTo(x, integer()))) checkTrue(!identical(as.numeric(1:10), updateObjectTo(x, integer()))) } -testUpdateObjectS4 <- function() { - setClass("A", - representation=representation( - x="numeric"), - prototype=list(x=1:5), - where=.GlobalEnv) - .__a__ <- new("A") - setClass("A", - representation=representation( - x="numeric", - y="character"), - where=.GlobalEnv) - checkException(validObject(.__a__), silent=TRUE) # now out-of-date - .__a__@x <- 1:5 - a <- updateObject(.__a__) - checkTrue(validObject(a)) - checkIdentical(1:5, a@x) - removeClass("A", where=.GlobalEnv) -} - -testUpdateObjectSetClass <- function() { +testUpdateObjectToSetClass <- function() { setClass("A", representation(x="numeric"), prototype=prototype(x=1:10), where=.GlobalEnv) a <- new("A") - checkTrue(identical(a,updateObject(a))) a1 <- new("A",x=10:1) checkTrue(identical(a, updateObjectTo(a, a1))) @@ -139,29 +66,28 @@ testUpdateESetMisc <- function() { opts <- options() options(warn=-1) - fp <- system.file("UnitTests", "VersionedClass_data", "devel", "sample.exprSet.rda", - package="Biobase") - load(fp) + + idx <- c("phenoData", "experimentData", "featureData") + fun <- function(nm) + isS4(eval(parse(text=paste(nm,"(obj)", sep="")))) + + load(system.file("UnitTests", "VersionedClass_data", "devel", + "sample.exprSet.rda", package="Biobase")) suppressMessages(obj <- as(sample.exprSet, "ExpressionSet")) checkTrue(validObject(obj, complete=TRUE)) - checkTrue(all(sapply(c("phenoData", "experimentData", "featureData"), - function(nm) isS4(eval(parse(text=paste(nm,"(obj)", sep=""))))))) + checkTrue(all(sapply(idx, fun))) - fp <- system.file("UnitTests", "VersionedClass_data", "devel", "sample.eSet.rda", - package="Biobase") - load(fp) + load(system.file("UnitTests", "VersionedClass_data", "devel", + "sample.eSet.rda", package="Biobase")) obj <- as(sample.eSet, "MultiSet") checkTrue(validObject(obj, complete=TRUE)) - checkTrue(all(sapply(c("phenoData", "experimentData", "featureData"), - function(nm) isS4(eval(parse(text=paste(nm,"(obj)", sep=""))))))) + checkTrue(all(sapply(idx, fun))) - fp <- system.file("UnitTests", "VersionedClass_data", "devel", "eset.rda", - package="Biobase") - load(fp) + load(system.file("UnitTests", "VersionedClass_data", "devel", "eset.rda", + package="Biobase")) obj <- as(eset, "ExpressionSet") checkTrue(validObject(obj, complete=TRUE)) - checkTrue(all(sapply(c("phenoData", "experimentData", "featureData"), - function(nm) isS4(eval(parse(text=paste(nm,"(obj)", sep=""))))))) + checkTrue(all(sapply(idx, fun))) options(opts) } @@ -171,20 +97,24 @@ options(warn=-1) on.exit(options(opts)) - rda <- list.files(system.file("UnitTests", "VersionedClass_data", package="Biobase"), - full.names=TRUE, recursive=TRUE, pattern="^([^(ExpressionSet)]).*\\.Rda") - for (nm in rda) { - cat(basename(nm), "\n") + rda <- dir(system.file("UnitTests", "VersionedClass_data", + package="Biobase"), full.names=TRUE, + recursive=TRUE, pattern="^([^(ExpressionSet)]).*\\.Rda") + + ok <- sapply(rda, function(nm) { env <- new.env(parent=emptyenv()) load(nm, env) - eapply(env, - function(elt) { - suppressMessages(obj <- updateObject(elt)) - checkTrue(isS4(obj)) - checkTrue(validObject(obj, complete=TRUE)) - }) - - } + tryCatch({ + eapply(env, function(elt) { + suppressMessages(obj <- updateObject(elt)) + checkTrue(isS4(obj)) + checkTrue(validObject(obj, complete=TRUE)) + }) + TRUE + }, error=function(...) FALSE) + }) + checkTrue(all(ok), + msg=sprintf("failed: '%s'", paste(rda[!ok], collapse="' '"))) } testUpdatePreviousExpressionSet <- function() { @@ -192,30 +122,42 @@ options(warn=-1) on.exit(options(opts)) - rda <- list.files(system.file("UnitTests", "VersionedClass_data", package="Biobase"), - full.names=TRUE, recursive=TRUE, pattern="^ExpressionSet.*\\.Rda") + rda <- dir(system.file("UnitTests", "VersionedClass_data", + package="Biobase"), full.names=TRUE, + recursive=TRUE, pattern="^ExpressionSet.*\\.Rda") - for (nm in rda) { + ok <- sapply(rda, function(nm) { env <- new.env(parent=emptyenv()) load(nm, env) - eapply(env, - function(elt) { - suppressMessages(obj <- updateObject(elt)) - checkTrue(validObject(obj, complete=TRUE)) - ## S4 - checkTrue(all(sapply(c("phenoData", "experimentData", "featureData"), - function(nm) isS4(eval(parse(text=paste(nm,"(obj)", sep=""))))))) - ## content - checkTrue(identical(exprs(obj), slot(elt, "assayData")[["exprs"]])) - checkTrue(identical(pData(phenoData(obj)), - slot(slot(elt, "phenoData"), "data"))) - checkTrue(identical(varMetadata(phenoData(obj)), - slot(slot(elt, "phenoData"), "varMetadata"))) - nms <- names(getSlots("MIAME")) - nms <- nms[!nms %in% ".__classVersion__"] - lapply(nms, function(nm) - checkTrue(identical(slot(experimentData(obj), nm), - slot(slot(elt, "experimentData"), nm)))) - }) - } + tryCatch({ + eapply(env, function(elt) { + suppressMessages(obj <- updateObject(elt)) + checkTrue(validObject(obj, complete=TRUE)) + ## S4 + idx <- c("phenoData", "experimentData", "featureData") + ok <- sapply(idx, function(nm) { + isS4(eval(parse(text=paste(nm,"(obj)", sep="")))) + }) + + checkTrue(all(ok)) + ## content + checkIdentical(exprs(obj), + slot(elt, "assayData")[["exprs"]]) + checkIdentical(pData(phenoData(obj)), + slot(slot(elt, "phenoData"), "data")) + checkIdentical(varMetadata(phenoData(obj)), + slot(slot(elt, "phenoData"), "varMetadata")) + nms <- names(getSlots("MIAME")) + nms <- nms[!nms %in% ".__classVersion__"] + lapply(nms, function(nm) + checkIdentical(slot(experimentData(obj), nm), + slot(slot(elt, "experimentData"), + nm))) + }) + TRUE + }, error=function(...) FALSE) + }) + + checkTrue(all(ok), + msg=sprintf("failed: '%s'", paste(rda[!ok], collapse="' '"))) } Binary files /tmp/23r_lGFEta/r-bioc-biobase-2.14.0/inst/UnitTests/VersionedClass_data/devel/MIAME.Rda and /tmp/OxmT1wIVc2/r-bioc-biobase-2.20.0/inst/UnitTests/VersionedClass_data/devel/MIAME.Rda differ Binary files /tmp/23r_lGFEta/r-bioc-biobase-2.14.0/inst/UnitTests/VersionedClass_data/devel/ScalarInteger.Rda and /tmp/OxmT1wIVc2/r-bioc-biobase-2.20.0/inst/UnitTests/VersionedClass_data/devel/ScalarInteger.Rda differ Binary files /tmp/23r_lGFEta/r-bioc-biobase-2.14.0/inst/UnitTests/VersionedClass_data/devel/ScalarLogical.Rda and /tmp/OxmT1wIVc2/r-bioc-biobase-2.20.0/inst/UnitTests/VersionedClass_data/devel/ScalarLogical.Rda differ Binary files /tmp/23r_lGFEta/r-bioc-biobase-2.14.0/inst/UnitTests/VersionedClass_data/devel/ScalarNumeric.Rda and /tmp/OxmT1wIVc2/r-bioc-biobase-2.20.0/inst/UnitTests/VersionedClass_data/devel/ScalarNumeric.Rda differ diff -Nru r-bioc-biobase-2.14.0/inst/UnitTests/combine_test.R r-bioc-biobase-2.20.0/inst/UnitTests/combine_test.R --- r-bioc-biobase-2.14.0/inst/UnitTests/combine_test.R 2011-10-31 23:32:00.000000000 +0000 +++ r-bioc-biobase-2.20.0/inst/UnitTests/combine_test.R 2013-04-03 22:22:34.000000000 +0000 @@ -17,54 +17,3 @@ checkTrue(all.equal(x, y)) } -testCombineThreeDF <- function() { - ## data.frame's are tricky, because c(df, list(...)) unlists df - x <- data.frame(x=1:5, - y=factor(letters[1:5], levels=letters[1:8]), - row.names=letters[1:5]) - y <- data.frame(z=3:7, - y=factor(letters[3:7], levels=letters[1:8]), - row.names=letters[3:7]) - w <- data.frame(w=4:8, - y=factor(letters[4:8], levels=letters[1:8]), - row.names=letters[4:8]) - res <- combine(w, x, y) - - e <- data.frame(w=c(4:8, rep(NA, 3)), - y=c(letters[c(4:8, 1:3)]), - x=c(4:5, rep(NA, 3), 1:3), - z=as.integer(c(4:7, rep(NA, 3), 3)), - row.names=letters[c(4:8, 1:3)]) - checkIdentical(e, res) -} - -testCombineDF_POSIXct <- function() -{ - ## class(x) can have length > 1 as in Sys.time() - t0 <- Sys.time() - df1 <- data.frame(i = 1:3, t = rep(t0, 3), row.names=letters[1:3]) - df2 <- data.frame(i = 1:3, t = c(t0, t0 + 500, t0 + 1000), - row.names=c("a", "d", "e")) - e <- data.frame(i = c(1L, 2L, 3L, 2L, 3L), - t = c(t0, t0, t0, t0 + 500, t0 + 1000), - row.names=c("a", "b", "c", "d", "e")) - res <- combine(df1, df2) - checkIdentical(e, res) -} - - -testCombineWithNamedArgs <- function() { - x <- data.frame(x=1:5, - y=factor(letters[1:5], levels=letters[1:8]), - row.names=letters[1:5]) - y <- data.frame(z=3:7, - y=factor(letters[3:7], levels=letters[1:8]), - row.names=letters[3:7]) - w <- data.frame(w=4:8, - y=factor(letters[4:8], levels=letters[1:8]), - row.names=letters[4:8]) - checkIdentical(combine(w, y, x), combine(w, x, y=y)) - checkIdentical(combine(w, y, x), combine(w, y=y, x)) - checkIdentical(combine(x, y, w), combine(w, y=y, x=x)) - checkIdentical(combine(x, y, w), combine(y=y, x=x, w)) -} diff -Nru r-bioc-biobase-2.14.0/inst/UnitTests/data.frame_test.R r-bioc-biobase-2.20.0/inst/UnitTests/data.frame_test.R --- r-bioc-biobase-2.14.0/inst/UnitTests/data.frame_test.R 2011-10-31 23:32:00.000000000 +0000 +++ r-bioc-biobase-2.20.0/inst/UnitTests/data.frame_test.R 1970-01-01 00:00:00.000000000 +0000 @@ -1,124 +0,0 @@ -checkDataFramesEqual <- function(obj1, obj2) { - checkTrue(identical(row.names(obj1), row.names(obj2))) - checkTrue(identical(colnames(obj1), colnames(obj2))) - checkTrue(all(sapply(colnames(obj1), function(nm) identical(obj1[[nm]], obj2[[nm]])))) -} - -testCombineDf <- function() { - ## no warnings - x <- data.frame(x=1:5,y=letters[1:5], row.names=letters[1:5]) - y <- data.frame(z=3:7,y=letters[c(3:5,1:2)], row.names=letters[3:7]) - z <- combine(x,y) - checkDataFramesEqual(x, z[1:5, colnames(x)]) - checkDataFramesEqual(y, z[3:7, colnames(y)]) - - ## an error -- content mismatch - x <- data.frame(x=1:3, y=letters[1:3], row.names=letters[1:3]) - y <- data.frame(z=2:4, y=letters[1:3], row.names=letters[2:4]) - checkException(suppressWarnings(combine(x,y)), silent=TRUE) - - ## a warning -- level coercion - oldw <- options("warn") - options(warn=2) - on.exit(options(oldw)) - x <- data.frame(x=1:2, y=letters[1:2], row.names=letters[1:2]) - y <- data.frame(z=2:3, y=letters[2:3], row.names=letters[2:3]) - checkException(combine(x,y), silent=TRUE) - options(oldw) - checkDataFramesEqual(suppressWarnings(combine(x,y)), - data.frame(x=c(1:2, NA), - y=letters[1:3], - z=c(NA, 2:3), - row.names=letters[1:3])) -} - -testCombineDfPreserveNumericRows <- function() { - dfA <- data.frame(label=rep("x", 2), row.names=1:2) - dfB <- data.frame(label=rep("x", 3), row.names=3:5) - dfAB <- combine(dfA, dfB) - ## preserve integer row names if possible - checkEquals(1:5, attr(dfAB, "row.names")) - - ## silently coerce row.names to character - dfC <- data.frame(label=rep("x", 2), row.names=as.character(3:4)) - dfAC <- combine(dfA, dfC) - checkEquals(as.character(1:4), attr(dfAC, "row.names")) -} - -testNoRow <- function() { - x <- data.frame(x=1,y=letters[1])[FALSE,] - y <- data.frame(z=1,y=letters[1])[FALSE,] - z <- combine(x,x) - checkTrue(identical(dim(z), as.integer(c(0,2)))) - x <- data.frame(x=1,y=letters[1])[FALSE,] - y <- data.frame(z=1,y=letters[1]) - z <- combine(x,y) - checkTrue(identical(dim(z), as.integer(c(1,3)))) - checkTrue(is.na(z$x)) - z <- combine(y,x) - checkTrue(identical(dim(z), as.integer(c(1,3)))) - checkTrue(is.na(z$x)) -} - -testOneRow <- function() { - x <- data.frame(x=1,y=letters[1], row.names=letters[1]) - y <- data.frame(z=3,y=letters[1], row.names=letters[2]) - z <- combine(x,y) - checkTrue(identical(dim(z), as.integer(c(2,3)))) - checkTrue(z$x[[1]]==1) - checkTrue(all(is.na(z$x[[2]]), is.na(z$z[[1]]))) - z <- combine(x,data.frame()) - checkTrue(identical(dim(z), as.integer(c(1,2)))) - checkTrue(all(z[,1:2]==x[,1:2])) - z <- combine(data.frame(),x) - checkTrue(identical(dim(z), as.integer(c(1,2)))) - checkTrue(all(z[,1:2]==x[,1:2])) -} - -testNoCol <- function() { - ## row.names - obj1 <- data.frame(numeric(20), row.names=letters[1:20])[,FALSE] - obj <- combine(obj1, obj1) - checkTrue(identical(obj, obj1)) - ## no row.names -- fails because row.names not recoverable from data.frame? - obj1 <- data.frame(numeric(20))[,FALSE] - obj <- combine(obj1, obj1) - checkTrue(all(dim(obj)==dim(obj1))) -} - -testNoCommonCols <- function() { - x <- data.frame(x=1:5, row.names=letters[1:5]) - y <- data.frame(y=3:7, row.names=letters[3:7]) - z <- combine(x,y) - checkTrue(all(dim(z)==as.integer(c(7,2)))) - checkTrue(all(z[1:5,"x"]==x[,"x"])) - checkTrue(all(z[3:7,"y"]==y[,"y"])) - checkTrue(all(which(is.na(z))==6:9)) -} - -testEmpty <- function() { - z <- combine(data.frame(), data.frame()) - checkTrue(identical(dim(z), as.integer(c(0,0)))) - x <- data.frame(x=1,y=letters[1], row.names=letters[1]) - z <- combine(x,data.frame()) - checkTrue(identical(dim(z), as.integer(c(1,2)))) - checkTrue(identical(z["a",1:2], x["a",1:2])) - z <- combine(data.frame(), x) - checkTrue(identical(dim(z), as.integer(c(1,2)))) - checkTrue(identical(z["a",1:2], x["a",1:2])) -} - -testAsIs <- function() { - x <- data.frame(x=I(1:5),y=I(letters[1:5]), row.names=letters[1:5]) - y <- data.frame(z=I(3:7),y=I(letters[3:7]), row.names=letters[3:7]) - z <- combine(x,y) - checkTrue(all(sapply(z, class)=="AsIs")) -} - -testColNamesSuffix <- function() { - obj1 <- data.frame(a=1:5, a.x=letters[1:5]) - obj2 <- data.frame(a=1:5, a.y=LETTERS[1:5], b=5:1) - obj <- combine(obj1, obj2) - checkDataFramesEqual(obj, - data.frame(a=1:5, a.x=letters[1:5], a.y=LETTERS[1:5], b=5:1)) -} diff -Nru r-bioc-biobase-2.14.0/inst/UnitTests/matrix_test.R r-bioc-biobase-2.20.0/inst/UnitTests/matrix_test.R --- r-bioc-biobase-2.14.0/inst/UnitTests/matrix_test.R 2011-10-31 23:32:00.000000000 +0000 +++ r-bioc-biobase-2.20.0/inst/UnitTests/matrix_test.R 1970-01-01 00:00:00.000000000 +0000 @@ -1,34 +0,0 @@ -testCombineMatrixDifferentModes <- function() { - m <- matrix(1:20, nrow=5, dimnames=list(LETTERS[1:5], letters[1:4])) - n <- matrix(as.numeric(1:20), - nrow=5, dimnames=list(LETTERS[1:5], letters[1:4])) - res <- combine(m, n) # modes coerced to same - checkEquals("numeric", mode(res)) - n <- matrix(as.character(1:20), - nrow=5, dimnames=list(LETTERS[1:5], letters[1:4])) - checkException(combine(m, n)) # modes differ -} - -testCombineMatrix <- function() { - ## dimnames - m <- matrix(1:20, nrow=5, dimnames=list(LETTERS[1:5], letters[1:4])) - checkEquals(m, combine(m, m)) - checkEquals(m, combine(m[1:3,], m[4:5,])) - checkEquals(m, combine(m[,1:3], m[,4, drop=FALSE])) - ## overlap - checkEquals(m, combine(m[1:3,], m[3:5,])) - checkEquals(m, combine(m[,1:3], m[,3:4])) - checkEquals(matrix(c(1:3, NA, NA, 6:8, NA, NA, 11:15, NA, NA, 18:20), - nrow=5, - dimnames=list(LETTERS[1:5], letters[1:4])), - combine(m[1:3,1:3], m[3:5, 3:4])) - ## row reordering - checkEquals(m[c(1,3,5,2,4),], combine(m[c(1,3,5),], m[c(2,4),])) - ## Exceptions - checkException(combine(m, matrix(0, nrow=5, ncol=4)), - silent=TRUE) # types differ - checkException(combine(m, matrix(0L, nrow=5, ncol=4)), - silent=TRUE) # attributes differ - m1 <- matrix(1:20, nrow=5) - checkException(combine(m, m1), silent=TRUE) # dimnames required -} diff -Nru r-bioc-biobase-2.14.0/inst/doc/BiobaseDevelopment.R r-bioc-biobase-2.20.0/inst/doc/BiobaseDevelopment.R --- r-bioc-biobase-2.14.0/inst/doc/BiobaseDevelopment.R 1970-01-01 00:00:00.000000000 +0000 +++ r-bioc-biobase-2.20.0/inst/doc/BiobaseDevelopment.R 2013-04-04 06:39:10.000000000 +0000 @@ -0,0 +1,230 @@ +### R code from vignette source 'BiobaseDevelopment.Rnw' + +################################################### +### code chunk number 1: Biobase +################################################### +options(width=69) +library(Biobase) + + +################################################### +### code chunk number 2: eSet-class +################################################### +getClass("eSet") + + +################################################### +### code chunk number 3: eSet-validity +################################################### +getValidity(getClass("eSet")) + + +################################################### +### code chunk number 4: ExpressionSet-initialize (eval = FALSE) +################################################### +## obj <- new("ExpressionSet", phenoData = new("AnnotatedDataFrame"), experimentData = new("MIAME"), annotation = character(), exprs = new("matrix")) + + +################################################### +### code chunk number 5: newAssayData (eval = FALSE) +################################################### +## assayDataNew("environment", elt) + + +################################################### +### code chunk number 6: assayData-storageMode +################################################### +data(sample.ExpressionSet) +storageMode(sample.ExpressionSet) +tryCatch(assayData(sample.ExpressionSet)$exprs <- log(exprs(sample.ExpressionSet)), + error=function(err) cat(conditionMessage(err))) +exprs(sample.ExpressionSet) <- log(exprs(sample.ExpressionSet)) + + +################################################### +### code chunk number 7: ExpressionSet-class +################################################### +getClass("ExpressionSet") +getValidity(getClass("ExpressionSet")) + + +################################################### +### code chunk number 8: SwirlSet-class +################################################### +setClass("SwirlSet", contains="eSet") + + +################################################### +### code chunk number 9: SwirlSet-initialize +################################################### +setMethod("initialize", "SwirlSet", + function(.Object, + R = new("matrix"), + G = new("matrix"), + Rb = new("matrix"), + Gb = new("matrix"), + ...) { + callNextMethod(.Object, + R=R, G=G, Rb=Rb, Gb=Gb, + ...) + }) + + +################################################### +### code chunk number 10: SwirlSet-initialize-2 +################################################### +setMethod("initialize", "SwirlSet", + function(.Object, + assayData=assayDataNew( + R=R, G=G, Rb=Rb, Gb=Gb), + R = new("matrix"), + G = new("matrix"), + Rb = new("matrix"), + Gb = new("matrix"), + ...) { + if (!missing(assayData) && + any(!missing(R), !missing(G), !missing(Rb), !missing(Gb))) { + warning("using 'assayData'; ignoring 'R', 'G', 'Rb', 'Gb'") + } + callNextMethod(.Object, assayData=assayData, ...) + }) + + +################################################### +### code chunk number 11: SwirlSet-new +################################################### +new("SwirlSet") + + +################################################### +### code chunk number 12: initialize-.Object (eval = FALSE) +################################################### +## setMethod("initialize", "MySet", +## function(.Object, ...) { +## .Object <- callNextMethod(.Object, ...) +## }) +## . + + +################################################### +### code chunk number 13: SwirlSet-validity +################################################### +setValidity("SwirlSet", function(object) { + assayDataValidMembers(assayData(object), c("R", "G", "Rb", "Gb")) +}) + + +################################################### +### code chunk number 14: validity-sometimes (eval = FALSE) +################################################### +## myFancyFunction <- function(obj) { +## assayData(obj) <- fancyAssaydData # obj invalid... +## phenoData(obj) <- justAsFancyPhenoData # but now valid +## validObject(obj) +## obj +## } + + +################################################### +### code chunk number 15: updateObject-eg +################################################### +data(sample.ExpressionSet) +classVersion(sample.ExpressionSet) +obj <- updateObject(sample.ExpressionSet) + + +################################################### +### code chunk number 16: isCurrent +################################################### +isCurrent(sample.ExpressionSet)[c("eSet", "ExpressionSet")] + + +################################################### +### code chunk number 17: MultiSet-obj +################################################### +setClass("MySet", + contains = "eSet", + prototype = prototype( + new("VersionedBiobase", + versions=c(classVersion("eSet"), MySet="1.0.0")))) +obj <- new("MySet") +classVersion(obj) + + +################################################### +### code chunk number 18: MultiSetRevised +################################################### +setClass("MySet", + contains = "eSet", + prototype = prototype( + new("VersionedBiobase", + versions=c(classVersion("eSet"), MySet="1.0.1")))) +isCurrent(obj) + + +################################################### +### code chunk number 19: updateObject-MultiSet +################################################### +setMethod("updateObject", signature(object="MySet"), + function(object, ..., verbose=FALSE) { + if (verbose) message("updateObject(object = 'MySet')") + object <- callNextMethod() + if (isCurrent(object)["MySet"]) return(object) + ## Create an updated instance. + if (!isVersioned(object)) + ## Radical surgery -- create a new, up-to-date instance + new("MySet", + assayData = updateObject(assayData(object), + ...., verbose=verbose), + phenoData = updateObject(phenoData(object), + ..., verbose=verbose), + experimentData = updateObject(experimentData(object), + ..., verbose=verbose), + annotation = updateObject(annotation(object), + ..., verbose=verbose)) + else { + ## Make minor changes, and update version by consulting class definition + classVersion(object)["MySet"] <- + classVersion("MySet")["MySet"] + object + } + }) + + +################################################### +### code chunk number 20: updateObject +################################################### +classVersion(updateObject(obj)) + + +################################################### +### code chunk number 21: classVersion-AnnotatedDataFrame +################################################### +classVersion(new("AnnotatedDataFrame")) + + +################################################### +### code chunk number 22: SwirlSet-version +################################################### +setClass("SwirlSet", contains = "eSet", + prototype = prototype( + new("VersionedBiobase", + versions=c(classVersion("eSet"), SwirlSet="1.0.0")))) +classVersion(new("SwirlSet")) + + +################################################### +### code chunk number 23: arbitraryClassVersions +################################################### +obj <- new("SwirlSet") +classVersion(obj)["MyID"] <- "0.0.1" +classVersion(obj) +classVersion(updateObject(obj)) + + +################################################### +### code chunk number 24: BiobaseDevelopment.Rnw:680-681 +################################################### +toLatex(sessionInfo()) + + diff -Nru r-bioc-biobase-2.14.0/inst/doc/BiobaseDevelopment.Rnw r-bioc-biobase-2.20.0/inst/doc/BiobaseDevelopment.Rnw --- r-bioc-biobase-2.14.0/inst/doc/BiobaseDevelopment.Rnw 2011-10-31 23:32:00.000000000 +0000 +++ r-bioc-biobase-2.20.0/inst/doc/BiobaseDevelopment.Rnw 2013-04-03 22:22:35.000000000 +0000 @@ -534,8 +534,9 @@ \Biobase{} introduces the \Rclass{Versioned} and \Rclass{VersionedBiobase} classes to facilitate this. These classes are incorporated into key \Biobase class definitions.\Biobase also -defines the \Rfunction{updateObject} generic and methods for -conveniently updating old objects to their new representation. +defines \Rmethod{updateObject} methods (the \Rfunction{updateObject} +generic function is defined in the \Rpackage{BiocGenerics} package) +for conveniently updating old objects to their new representation. <>= data(sample.ExpressionSet) classVersion(sample.ExpressionSet) Binary files /tmp/23r_lGFEta/r-bioc-biobase-2.14.0/inst/doc/BiobaseDevelopment.pdf and /tmp/OxmT1wIVc2/r-bioc-biobase-2.20.0/inst/doc/BiobaseDevelopment.pdf differ diff -Nru r-bioc-biobase-2.14.0/inst/doc/Bioconductor.R r-bioc-biobase-2.20.0/inst/doc/Bioconductor.R --- r-bioc-biobase-2.14.0/inst/doc/Bioconductor.R 1970-01-01 00:00:00.000000000 +0000 +++ r-bioc-biobase-2.20.0/inst/doc/Bioconductor.R 2013-04-04 06:39:11.000000000 +0000 @@ -0,0 +1,8 @@ +### R code from vignette source 'Bioconductor.Rnw' + +################################################### +### code chunk number 1: Bioconductor.Rnw:91-92 +################################################### +sessionInfo() + + Binary files /tmp/23r_lGFEta/r-bioc-biobase-2.14.0/inst/doc/Bioconductor.pdf and /tmp/OxmT1wIVc2/r-bioc-biobase-2.20.0/inst/doc/Bioconductor.pdf differ diff -Nru r-bioc-biobase-2.14.0/inst/doc/ExpressionSetIntroduction.R r-bioc-biobase-2.20.0/inst/doc/ExpressionSetIntroduction.R --- r-bioc-biobase-2.14.0/inst/doc/ExpressionSetIntroduction.R 1970-01-01 00:00:00.000000000 +0000 +++ r-bioc-biobase-2.20.0/inst/doc/ExpressionSetIntroduction.R 2013-04-04 06:39:15.000000000 +0000 @@ -0,0 +1,218 @@ +### R code from vignette source 'ExpressionSetIntroduction.Rnw' + +################################################### +### code chunk number 1: init +################################################### +options(width=65) + + +################################################### +### code chunk number 2: install-pkg (eval = FALSE) +################################################### +## source("http://bioconductor.org/biocLite.R") +## biocLite(c("Biobase")) + + +################################################### +### code chunk number 3: loadlib +################################################### +library("Biobase") + + +################################################### +### code chunk number 4: convert (eval = FALSE) +################################################### +## library(convert) +## as(object, "ExpressionSet") + + +################################################### +### code chunk number 5: read-table-geneData +################################################### +dataDirectory <- system.file("extdata", package="Biobase") +exprsFile <- file.path(dataDirectory, "exprsData.txt") +exprs <- as.matrix(read.table(exprsFile, header=TRUE, sep="\t", + row.names=1, + as.is=TRUE)) + + +################################################### +### code chunk number 6: exprsFile (eval = FALSE) +################################################### +## exprsFile <- "c:/path/to/exprsData.txt" + + +################################################### +### code chunk number 7: geneData-peak +################################################### +class(exprs) +dim(exprs) +colnames(exprs) +head(exprs[,1:5]) + + +################################################### +### code chunk number 8: ExpressionSet-basic +################################################### +minimalSet <- ExpressionSet(assayData=exprs) + + +################################################### +### code chunk number 9: pData +################################################### +pDataFile <- file.path(dataDirectory, "pData.txt") +pData <- read.table(pDataFile, + row.names=1, header=TRUE, sep="\t") +dim(pData) +rownames(pData) +summary(pData) + + +################################################### +### code chunk number 10: geneCovariate-geneData-name-match +################################################### +all(rownames(pData)==colnames(exprs)) + + +################################################### +### code chunk number 11: colnames +################################################### +names(pData) + + +################################################### +### code chunk number 12: sapplyClasses +################################################### +sapply(pData, class) + + +################################################### +### code chunk number 13: simpleSubsetting +################################################### +pData[c(15, 20), c("gender", "type")] +pData[pData$score>0.8,] + + +################################################### +### code chunk number 14: metadata-create +################################################### +metadata <- data.frame(labelDescription= + c("Patient gender", + "Case/control status", + "Tumor progress on XYZ scale"), + row.names=c("gender", "type", "score")) + + +################################################### +### code chunk number 15: AnnotatedDataFrame +################################################### +phenoData <- new("AnnotatedDataFrame", + data=pData, varMetadata=metadata) +phenoData + + +################################################### +### code chunk number 16: AnnotatedDataFrame-subset +################################################### +head(pData(phenoData)) +phenoData[c("A","Z"),"gender"] +pData(phenoData[phenoData$score>0.8,]) + + +################################################### +### code chunk number 17: annotation +################################################### +annotation <- "hgu95av2" + + +################################################### +### code chunk number 18: R.MIAME +################################################### +experimentData <- new("MIAME", + name="Pierre Fermat", + lab="Francis Galton Lab", + contact="pfermat@lab.not.exist", + title="Smoking-Cancer Experiment", + abstract="An example ExpressionSet", + url="www.lab.not.exist", + other=list( + notes="Created from text files" + )) + + +################################################### +### code chunk number 19: ExpressionSetFinally +################################################### +exampleSet <- ExpressionSet(assayData=exprs, + phenoData=phenoData, + experimentData=experimentData, + annotation="hgu95av2") + + +################################################### +### code chunk number 20: ExpressionSet-minimal +################################################### +minimalSet <- ExpressionSet(assayData=exprs) + + +################################################### +### code chunk number 21: helpExpressionSet (eval = FALSE) +################################################### +## help("ExpressionSet-class") + + +################################################### +### code chunk number 22: showExpressionSet +################################################### +exampleSet + + +################################################### +### code chunk number 23: usingDollar +################################################### +exampleSet$gender[1:5] +exampleSet$gender[1:5] == "Female" + + +################################################### +### code chunk number 24: featureNames +################################################### +featureNames(exampleSet)[1:5] + + +################################################### +### code chunk number 25: sampleNames +################################################### +sampleNames(exampleSet)[1:5] +varLabels(exampleSet) + + +################################################### +### code chunk number 26: exprs +################################################### +mat <- exprs(exampleSet) +dim(mat) + + +################################################### +### code chunk number 27: first10 +################################################### +vv <- exampleSet[1:5, 1:3] +dim(vv) +featureNames(vv) +sampleNames(vv) + + +################################################### +### code chunk number 28: males +################################################### +males <- exampleSet[ , exampleSet$gender == "Male"] +males + + +################################################### +### code chunk number 29: ExpressionSetIntroduction.Rnw:489-490 +################################################### +toLatex(sessionInfo()) + + diff -Nru r-bioc-biobase-2.14.0/inst/doc/ExpressionSetIntroduction.Rnw r-bioc-biobase-2.20.0/inst/doc/ExpressionSetIntroduction.Rnw --- r-bioc-biobase-2.14.0/inst/doc/ExpressionSetIntroduction.Rnw 2011-10-31 23:32:00.000000000 +0000 +++ r-bioc-biobase-2.20.0/inst/doc/ExpressionSetIntroduction.Rnw 2013-04-03 22:22:35.000000000 +0000 @@ -452,14 +452,11 @@ varLabels(exampleSet) @ %% -Extract the expression matrix and the \Rclass{AnnotatedDataFrame} of -sample information using \Rfunction{exprs} and \Rfunction{phenoData}, -respectively: +Extract the expression matrix of +sample information using \Rfunction{exprs}: <>= mat <- exprs(exampleSet) dim(mat) -adf <- phenoData(exampleSet) -adf @ \subsubsection{Subsetting} Binary files /tmp/23r_lGFEta/r-bioc-biobase-2.14.0/inst/doc/ExpressionSetIntroduction.pdf and /tmp/OxmT1wIVc2/r-bioc-biobase-2.20.0/inst/doc/ExpressionSetIntroduction.pdf differ diff -Nru r-bioc-biobase-2.14.0/inst/doc/HowTo.R r-bioc-biobase-2.20.0/inst/doc/HowTo.R --- r-bioc-biobase-2.14.0/inst/doc/HowTo.R 1970-01-01 00:00:00.000000000 +0000 +++ r-bioc-biobase-2.20.0/inst/doc/HowTo.R 2013-04-04 06:39:15.000000000 +0000 @@ -0,0 +1,8 @@ +### R code from vignette source 'HowTo.Rnw' + +################################################### +### code chunk number 1: HowTo.Rnw:86-87 +################################################### +sessionInfo() + + Binary files /tmp/23r_lGFEta/r-bioc-biobase-2.14.0/inst/doc/HowTo.pdf and /tmp/OxmT1wIVc2/r-bioc-biobase-2.20.0/inst/doc/HowTo.pdf differ diff -Nru r-bioc-biobase-2.14.0/inst/doc/Qviews.R r-bioc-biobase-2.20.0/inst/doc/Qviews.R --- r-bioc-biobase-2.14.0/inst/doc/Qviews.R 1970-01-01 00:00:00.000000000 +0000 +++ r-bioc-biobase-2.20.0/inst/doc/Qviews.R 2013-04-04 06:39:18.000000000 +0000 @@ -0,0 +1,120 @@ +### R code from vignette source 'Qviews.Rnw' + +################################################### +### code chunk number 1: doa +################################################### +if (!("Biobase" %in% search())) library(Biobase) +if (!("ALL" %in% search())) library(ALL) +if (!("ALL" %in% objects())) data(ALL) + + +################################################### +### code chunk number 2: getaEF (eval = FALSE) +################################################### +## library(Biobase) +## library(ALL) +## data(ALL) +## ALL + + +################################################### +### code chunk number 3: mkprov +################################################### +dataSource = function(dsn) { + if (!is(dsn, "character")) dsn = try(deparse(substitute(dsn))) + if (inherits(dsn, "try-error")) stop("can't parse dsn arg") + dd = data()$results + if (is.na(match(dsn, dd[,"Item"]))) return(NULL) + paste("package:", dd[ dd[,"Item"] == dsn, "Package" ], sep="") +} + + + + +################################################### +### code chunk number 4: newmeth +################################################### +setGeneric("peek", function(x,maxattr=10)standardGeneric("peek")) +setMethod("peek", c("eSet", "numeric"), function(x,maxattr=10) { + ds = dataSource(deparse(substitute(x))) + if (!is.null(ds)) ds = paste(" [from ", ds, "]", sep="") + else ds = "" + cat(deparse(substitute(x)), ds, ":\n", sep="") + cat("Platform annotation: ", annotation(x),"\n") + cat("primary assay results are:\n") + print(dim(x)) + cat("sample attributes are:\n") + vn = rownames(varMetadata(x)) + ld = substr(varMetadata(x)$labelDescription,1,50) + dd = data.frame("labelDescription[truncated]"=ld) + rownames(dd) = vn + if ((ndd <- nrow(dd)) <= maxattr) show(dd) + else { + cat("first", maxattr, "of", ndd, "attributes:\n") + show(dd[1:maxattr,,drop=FALSE]) + } + cat("----------\n") + cat("use varTable to see values/freqs of all sample attributes\n") + cat("----------\n") +}) +setMethod("peek", c("eSet", "missing"), function(x,maxattr=10) { + ds = dataSource(deparse(substitute(x))) + if (!is.null(ds)) ds = paste(" [from ", ds, "]", sep="") + else ds = "" + cat(deparse(substitute(x)), ds, ":\n", sep="") + cat("Platform annotation: ", annotation(x),"\n") + cat("primary assay results are:\n") + print(dim(x)) + cat("sample attributes are:\n") + vn = rownames(varMetadata(x)) + ld = substr(varMetadata(x)$labelDescription,1,50) + dd = data.frame("labelDescription[truncated]"=ld) + rownames(dd) = vn + if ((ndd <- nrow(dd)) <= maxattr) show(dd) + else { + cat("first", maxattr, "of", ndd, "attributes:\n") + show(dd[1:maxattr,,drop=FALSE]) + } + cat("----------\n") + cat("use varTable to see values/freqs of all sample attributes\n") + cat("----------\n") +}) +setGeneric("varTable", function(x, full=FALSE, max=Inf) standardGeneric("varTable")) +setMethod("varTable", c("eSet", "missing", "ANY"), function(x, full=FALSE, max=Inf) varTable(x, FALSE, max)) +setMethod("varTable", c("eSet", "logical", "ANY"), function(x, full=FALSE, max=Inf) { + ans = lapply( names(pData(x)), function(z)table(x[[z]]) ) + tans = lapply(ans, names) + kp = 1:min(max,length(tans)) + if (!full) ans = sapply(tans, selectSome, 3)[kp] + else ans = tans[kp] + names(ans) = names(pData(x))[kp] + ans +}) +setGeneric("varNames", function(x) standardGeneric("varNames")) +setMethod("varNames", "eSet", function(x) names(pData(x))) + + +################################################### +### code chunk number 5: lka +################################################### +peek(ALL) + + +################################################### +### code chunk number 6: lkv +################################################### +varNames(ALL) + + +################################################### +### code chunk number 7: lkvn +################################################### +varTable(ALL, max=4) + + +################################################### +### code chunk number 8: lkvn +################################################### +varTable(ALL, full=TRUE, max=4) + + Binary files /tmp/23r_lGFEta/r-bioc-biobase-2.14.0/inst/doc/Qviews.pdf and /tmp/OxmT1wIVc2/r-bioc-biobase-2.20.0/inst/doc/Qviews.pdf differ diff -Nru r-bioc-biobase-2.14.0/inst/doc/esApply.R r-bioc-biobase-2.20.0/inst/doc/esApply.R --- r-bioc-biobase-2.14.0/inst/doc/esApply.R 1970-01-01 00:00:00.000000000 +0000 +++ r-bioc-biobase-2.20.0/inst/doc/esApply.R 2013-04-04 06:39:20.000000000 +0000 @@ -0,0 +1,57 @@ +### R code from vignette source 'esApply.Rnw' + +################################################### +### code chunk number 1: R.hide +################################################### +library(Biobase) +data(sample.ExpressionSet) + + +################################################### +### code chunk number 2: R +################################################### +print(sample.ExpressionSet) +print(exprs(sample.ExpressionSet)[1,]) +print(pData(sample.ExpressionSet)[1:2,1:3]) + + +################################################### +### code chunk number 3: R +################################################### +print(rbind(exprs(sample.ExpressionSet[1,]), +sex <- t(pData(sample.ExpressionSet))[1,])) + + +################################################### +### code chunk number 4: R +################################################### +medContr <- function( y, x ) { + ys <- split(y,x) + median(ys[[1]]) - median(ys[[2]]) +} + + +################################################### +### code chunk number 5: R +################################################### +print(apply(exprs(sample.ExpressionSet[1,,drop=F]), 1, + medContr, pData(sample.ExpressionSet)[["sex"]])) + + +################################################### +### code chunk number 6: R +################################################### +medContr1 <- function(y) { + ys <- split(y,sex) + median(ys[[1]]) - median(ys[[2]]) +} + +print(esApply( sample.ExpressionSet, 1, medContr1)[1]) + + +################################################### +### code chunk number 7: esApply.Rnw:126-127 +################################################### +sessionInfo() + + Binary files /tmp/23r_lGFEta/r-bioc-biobase-2.14.0/inst/doc/esApply.pdf and /tmp/OxmT1wIVc2/r-bioc-biobase-2.20.0/inst/doc/esApply.pdf differ diff -Nru r-bioc-biobase-2.14.0/man/annotation.Rd r-bioc-biobase-2.20.0/man/annotation.Rd --- r-bioc-biobase-2.14.0/man/annotation.Rd 2011-10-31 23:31:58.000000000 +0000 +++ r-bioc-biobase-2.20.0/man/annotation.Rd 1970-01-01 00:00:00.000000000 +0000 @@ -1,29 +0,0 @@ -\name{annotation} -\alias{annotation} -\alias{annotation<-} - -\title{Annotate eSet data.} -\description{ -This generic function handles methods for adding and retrieving -`annotation' and `description' information for eSets. An annotation is the name of the file describing the chip used for the experiment. -} -\usage{ -annotation(object) -annotation(object) <- value - -} -\arguments{ - \item{object}{Object derived from class eSet} - \item{value}{character(1) describing the chip from which the eSet data - is obtained} -} -\value{ - \code{annotation(object)} returns a character vector indicating the - annotation package. -} -\author{Biocore} - -\seealso{\code{\link{eSet-class}}, - \code{\link{ExpressionSet-class}}, \code{\link{SnpSet-class}}} - -\keyword{manip} diff -Nru r-bioc-biobase-2.14.0/man/biocReposList.Rd r-bioc-biobase-2.20.0/man/biocReposList.Rd --- r-bioc-biobase-2.14.0/man/biocReposList.Rd 2011-10-31 23:31:58.000000000 +0000 +++ r-bioc-biobase-2.20.0/man/biocReposList.Rd 1970-01-01 00:00:00.000000000 +0000 @@ -1,41 +0,0 @@ -\name{biocReposList} -\alias{biocReposList} - -\title{Return a list of Bioconductor package repositories} -\description{ - WARNING: The \code{biocReposList} function is deprecated! - - This function returns a named character vector of Bioconductor package - repositories. - - The vector can be used as the \code{repos} argument to - \code{install.packages} and friends. -} -\usage{ -biocReposList() -} - -\details{ - The repository URLs are hardcoded for each release. -} -\value{ - \item{bioc}{URL for Bioc software package repository} - \item{aData}{URL for Bioc annotation data package repository} - \item{eData}{URL for Bioc experiment data package repository} - \item{extra}{URL for Bioc extra repository} - \item{cran}{URL for CRAN package repository.} -} -\author{S. Falcon} -\examples{ -## This function is deprecated. Please use biocLite() to install packages: -if (interactive()) { - source("http://bioconductor.org/biocLite.R") - biocLite("hgu95av2.db") -} -## If you really need to get the list of Bioconductor package repositories -## (like biocReposList() does), then do: -source("http://bioconductor.org/biocLite.R") -biocinstallRepos() # PLEASE USE THIS, NOT biocReposList() -} -\keyword{utilities} - diff -Nru r-bioc-biobase-2.14.0/man/class.AnnotatedDataFrame.Rd r-bioc-biobase-2.20.0/man/class.AnnotatedDataFrame.Rd --- r-bioc-biobase-2.14.0/man/class.AnnotatedDataFrame.Rd 2011-10-31 23:31:58.000000000 +0000 +++ r-bioc-biobase-2.20.0/man/class.AnnotatedDataFrame.Rd 2013-04-03 22:22:31.000000000 +0000 @@ -184,7 +184,7 @@ AnnotatedDataFrame() AnnotatedDataFrame(data=df) -AnnotatedDataFrame(data=df, varMetaData=metaData) +AnnotatedDataFrame(data=df, varMetadata=metaData) as(df, "AnnotatedDataFrame") obj <- AnnotatedDataFrame() diff -Nru r-bioc-biobase-2.14.0/man/class.ExpressionSet.Rd r-bioc-biobase-2.20.0/man/class.ExpressionSet.Rd --- r-bioc-biobase-2.14.0/man/class.ExpressionSet.Rd 2011-10-31 23:31:58.000000000 +0000 +++ r-bioc-biobase-2.20.0/man/class.ExpressionSet.Rd 2013-04-03 22:22:31.000000000 +0000 @@ -31,31 +31,79 @@ \code{\link{eSet}}, and requires a matrix named \code{exprs} as assayData member. } + +\usage{ +## Instance creation +ExpressionSet(assayData, + phenoData=annotatedDataFrameFrom(assayData, byrow=FALSE), + featureData=annotatedDataFrameFrom(assayData, byrow=TRUE), + experimentData=new("MIAME"), annotation=character(), + protocolData=annotatedDataFrameFrom(assayData, byrow=FALSE), + ...) + +## Additional methods documented below +} + +\arguments{ + + \item{assayData}{A \code{matrix} of expression values, or an + \code{environment}. + + When \code{assayData} is a \code{matrix}, the rows represent probe + sets (\sQuote{features} in \code{ExpressionSet} parlance). Columns + represent samples. When present, row names identify features and + column names identify samples. Row and column names must be unique, + and consistent with row names of \code{featureData} and + \code{phenoData}, respectively. The assay data can be retrieved with + \code{exprs()}. + + When \code{assayData} is an environment, it contains identically + dimensioned matrices like that described in the previous + paragraph. One of the elements of the environment must be named + \sQuote{exprs}; this element is returned with \code{exprs()}. + + } + + \item{phenoData}{An optional \code{data.frame} or + \code{AnnotatedDataFrame} containing information about each + sample. The number of rows in \code{phenoData} must match the number + of columns in \code{assayData}. Row names of \code{phenoData} must + match column names of the matrix / matricies in \code{assayData}.} + + \item{featureData}{An optional \code{data.frame} or + \code{AnnotatedDataFrame} containing information about each + feature. The number of rows in \code{featureData} must match the + number of rows in \code{assayData}. Row names of \code{featureData} + must match row names of the matrix / matricies in \code{assayData}.} + + \item{experimentData}{An optional \code{MIAME} instance with meta-data + (e.g., the lab and resulting publications from the analysis) about + the experiment.} + + \item{annotation}{A \code{character} describing the platform on which + the samples were assayed. This is often the name of a Bioconductor + chip annotation package, which facilitated down-stream analysis.} + + \item{protocolData}{An optional \code{AnnotatedDataFrame} containing + equipment-generated information about protocols. The number of rows + and row names of \code{protocolData} must agree with the dimension + and column names of \code{assayData}.} + + \item{\dots}{Additional arguments, passed to + \code{new("ExpressionSet", ...)} and available for classes that extend + \code{ExpressionSet}. + } + +} + \section{Extends}{ Directly extends class \code{\link{eSet}}. } \section{Creating Objects}{ \code{ExpressionSet} instances are usually created through + \code{ExpressionSet()}. - \code{ExpressionSet()} - - \code{ExpressionSet(assayData, - phenoData=annotatedDataFrameFrom(assayData, byrow=FALSE), - featureData=annotatedDataFrameFrom(assayData, byrow=TRUE), - experimentData=new("MIAME"), annotation=character(), - protocolData=annotatedDataFrameFrom(assayData, byrow=FALSE), - ...) - } - This creates an \code{ExpressionSet} with \code{assayData} provided - explicitly. In this form, the only required named argument is - \code{assayData}. \code{assayData} can be \code{matrix} (a matrix of - expression data, with features corresponding to rows and samples - to columns) or an \code{environment} that contains \code{exprs}. - - \code{phenoData}, \code{featureData}, \code{experimentData}, - \code{annotation}, and \code{protocolData} can be missing, in which case - they are assigned default values. } \section{Slots}{ Inherited from \code{eSet}: @@ -63,7 +111,7 @@ \item{\code{assayData}:}{Contains matrices with equal dimensions, and with column number equal to \code{nrow(phenoData)}. \code{assayData} must contain a matrix - \code{exprs} with rows represening features (e.g., reporters) + \code{exprs} with rows representing features (e.g., probe sets) and columns representing samples. Additional matrices of identical size (e.g., representing measurement errors) may also be included in \code{assayData}. Class:\code{\link{AssayData-class}}} @@ -160,7 +208,6 @@ # information about assay and sample data featureNames(sample.ExpressionSet)[1:10] sampleNames(sample.ExpressionSet)[1:5] -phenoData(sample.ExpressionSet) experimentData(sample.ExpressionSet) # subset: first 10 genes, samples 2, 4, and 10 diff -Nru r-bioc-biobase-2.14.0/man/class.eSet.Rd r-bioc-biobase-2.20.0/man/class.eSet.Rd --- r-bioc-biobase-2.14.0/man/class.eSet.Rd 2011-10-31 23:31:58.000000000 +0000 +++ r-bioc-biobase-2.20.0/man/class.eSet.Rd 2013-04-03 22:22:31.000000000 +0000 @@ -22,6 +22,10 @@ \alias{combine,eSet,eSet-method} \alias{description,eSet-method} \alias{description<-,eSet,MIAME-method} +\alias{dimnames} +\alias{dimnames<-} +\alias{dimnames,eSet-method} +\alias{dimnames<-,eSet-method} \alias{dim,eSet-method} \alias{dims,eSet-method} \alias{experimentData,eSet-method} @@ -136,6 +140,9 @@ \item{\code{featureNames(object)}, \code{featureNames(object) <- value}:}{Coordinate accessing and setting of feature names (e.g, genes, probes) in \code{assayData}.} + \item{\code{dimnames(object)}, \code{dimnames(object) <- + value}:}{Also \code{rownames} and \code{colnames}; access and set + feature and sample names.} \item{\code{dims(object)}:}{Access the common dimensions (\code{dim}) or column numbers (\code{ncol}), or dimensions of all members (\code{dims}) of \code{assayData}.} diff -Nru r-bioc-biobase-2.14.0/man/combine.Rd r-bioc-biobase-2.20.0/man/combine.Rd --- r-bioc-biobase-2.14.0/man/combine.Rd 2011-10-31 23:31:58.000000000 +0000 +++ r-bioc-biobase-2.20.0/man/combine.Rd 1970-01-01 00:00:00.000000000 +0000 @@ -1,109 +0,0 @@ -\name{combine} -\alias{combine} -\alias{combine,ANY,missing-method} -\alias{combine,data.frame,data.frame-method} -\alias{combine,matrix,matrix-method} -\concept{combine phenoData} - -\title{Methods for Function combine in Package `Biobase'} -\description{ - This generic function handles methods for combining or merging different - Bioconductor data structures. It should, given an arbitrary number of - arguments of the same class (possibly by inheritance), combine them into - a single instance in a sensible way (some methods may only combine 2 - objects, ignoring \code{...} in the argument list; because Bioconductor - data structures are complicated, check carefully that \code{combine} - does as you intend). -} -\usage{ -combine(x, y, ...) -} -\arguments{ - \item{x}{One of the values. } - \item{y}{A second value. } - \item{\dots}{Any other objects of the same class as \code{x} and \code{y}. } -} -\details{ - There are two basic combine strategies. One is an intersection - strategy. The returned value should only have rows (or columns) that - are found in all input data objects. The union strategy says that the - return value will have all rows (or columns) found in any one of the - input data objects (in which case some indication of what to use for - missing values will need to be provided). - - These functions and methods are currently under construction. Please - let us know if there are features that you require. -} -\section{Methods}{ - \describe{ - \item{\code{combine(x=ANY, missing)}}{Return the first (x) argument - unchanged.} - \item{\code{combine(data.frame, data.frame)}}{Combines two - \code{data.frame} objects so that the resulting \code{data.frame} - contains all rows and columns of the original objects. Rows and - columns in the returned value are unique, that is, a row or column - represented in both arguments is represented only once in the - result. To perform this operation, \code{combine} makes sure that data - in shared rows and columns are identical in the two - data.frames. Data differences in shared rows and columns usually cause an - error. \code{combine} issues a warning when a column is a - \code{\link{factor}} and the levels of the factor in the two - data.frames are different.} - \item{\code{combine(matrix, matrix)}}{Combined two \code{matrix} - objects so that the resulting \code{matrix} contains all rows and - columns of the original objects. Both matricies must have - \code{dimnames}. Rows and columns in the returned - value are unique, that is, a row or column represented in both - arguments is represented only once in the result. To perform this - operation, \code{combine} makes sure that data in shared rows and - columns are all equal in the two matricies.} - } - Additional \code{combine} methods are defined for - \code{\link{AnnotatedDataFrame}}, - \code{\link{AssayData}}, \code{\link{MIAME}}, and \code{\link{eSet}} - classes and subclasses. -} -\value{ - A single value of the same class as the most specific common ancestor - (in class terms) of the input values. This will contain the - appropriate combination of the data in the input values. -} -\author{Biocore} - -\seealso{\code{\link{merge}}} - -\examples{ - x <- data.frame(x=1:5, - y=factor(letters[1:5], levels=letters[1:8]), - row.names=letters[1:5]) - y <- data.frame(z=3:7, - y=factor(letters[3:7], levels=letters[1:8]), - row.names=letters[3:7]) - combine(x,y) - - w <- data.frame(w=4:8, - y=factor(letters[4:8], levels=letters[1:8]), - row.names=letters[4:8]) - combine(w, x, y) - - # y is converted to 'factor' with different levels - df1 <- data.frame(x=1:5,y=letters[1:5], row.names=letters[1:5]) - df2 <- data.frame(z=3:7,y=letters[3:7], row.names=letters[3:7]) - try(combine(df1, df2)) # fails - # solution 1: ensure identical levels - y1 <- factor(letters[1:5], levels=letters[1:7]) - y2 <- factor(letters[3:7], levels=letters[1:7]) - df1 <- data.frame(x=1:5,y=y1, row.names=letters[1:5]) - df2 <- data.frame(z=3:7,y=y2, row.names=letters[3:7]) - combine(df1, df2) - # solution 2: force column to be 'character' - df1 <- data.frame(x=1:5,y=I(letters[1:5]), row.names=letters[1:5]) - df2 <- data.frame(z=3:7,y=I(letters[3:7]), row.names=letters[3:7]) - combine(df1, df2) - - m <- matrix(1:20, nrow=5, dimnames=list(LETTERS[1:5], letters[1:4])) - combine(m[1:3,], m[4:5,]) - combine(m[1:3, 1:3], m[3:5, 3:4]) # overlap -} - -\keyword{manip} diff -Nru r-bioc-biobase-2.14.0/man/defunct.Rd r-bioc-biobase-2.20.0/man/defunct.Rd --- r-bioc-biobase-2.14.0/man/defunct.Rd 2011-10-31 23:31:58.000000000 +0000 +++ r-bioc-biobase-2.20.0/man/defunct.Rd 2013-04-03 22:22:31.000000000 +0000 @@ -1,4 +1,4 @@ -\name{Deprecated} +\name{Deprecated and Defunct} \title{Biobase Deprecated and Defunct} \alias{class:annotatedDataset} @@ -59,6 +59,7 @@ \alias{l2e} +\alias{biocReposList} \description{ The function, class, or data object you have asked for has been deprecated or made defunct. diff -Nru r-bioc-biobase-2.14.0/man/updateObject.Rd r-bioc-biobase-2.20.0/man/updateObject.Rd --- r-bioc-biobase-2.14.0/man/updateObject.Rd 2011-10-31 23:31:58.000000000 +0000 +++ r-bioc-biobase-2.20.0/man/updateObject.Rd 1970-01-01 00:00:00.000000000 +0000 @@ -1,124 +0,0 @@ -\name{updateObject} -\alias{updateObject} -\alias{updateObjectTo} - -\alias{updateObject,ANY-method} -\alias{updateObject,list-method} -\alias{updateObject,environment-method} -\alias{updateObjectTo,ANY,ANY-method} - -\alias{updateObjectFromSlots} -\alias{getObjectSlots} - -\title{Update an object to its current class definition} -\description{ - These generic functions return an instance of \code{object} updated to - its current class definition (or to the class definition of - \code{template}, in the case of \code{updateObjectTo}). - - Updating objects is primarily useful when an object has been - serialized (e.g., stored to disk) for some time (e.g., months), and the - class definition has in the mean time changed. Because of the changed - class definition, the serialized instance is no longer valid. - - \code{updateObject} requires that the class of the returned object be - the same as the class of the argument \code{object}, and that the - object is valid (see \code{\link[methods]{validObject}}). By default, - \code{updateObject} has the following behaviors: - \describe{ - \item{\code{updateObject(ANY, \dots, verbose=FALSE)}}{By default, - \code{updateObject} uses heuristic methods to determine whether - the object should be the `new' S4 type (introduced in R 2.4.0), - but is not. If the heuristics indicate an update is required, - the \code{\link{updateObjectFromSlots}} function tries to update the - object. The default method returns the original S4 object or the successfully - updated object, or issues an error if an update is required but - not possible. The optional - named argument \code{verbose} causes a message to be printed describing - the action. Arguments \code{\dots} are passed to \code{link{updateObjectFromSlots}}.} - \item{\code{updateObject(list, \dots, verbose=FALSE)}}{Visit each element in \code{list}, - applying \code{updateObject(list[[elt]], \dots, verbose=verbose)}.} - \item{\code{updateObject(environment, \dots, verbose=FALSE)}}{Visit - each element in \code{environment}, applying - \code{updateObject(environment[[elt]], \dots, verbose=verbose)}} - } - - \code{updateObjectTo} requires that the class of the returned object - be the same as the class of the \code{template} argument, and that the - object is valid. Usually, updating proceeds by modifying slots in - \code{template} with information from \code{object}, and returning - \code{template}. Use \code{\link{as}} to coerce an object from one - type to another; \code{updateObjectTo} might be useful to update a - virtual superclass. By default, \code{updateObjectTo} has the following - behavior: - \describe{ - \item{\code{updateObjectTo(ANY-object,ANY-template)}}{Attempt \code{as(ANY-object,class(ANY-template))}.} - } - - Sample methods are illustrated below. - - \code{updateObjectFromSlots(object, objclass = class(object), \dots, verbose=FALSE)} is a - utility function that identifies the intersection of slots defined in - the \code{object} instance and \code{objclass} definition. The - corresponding elements in \code{object} are then updated (with - \code{updateObject(elt, \dots, verbose=verbose)}) and used as arguments to - a call to \code{new(class, \dots)}, with \code{\dots} replaced by slots - from the original object. If this fails, \code{updateObjectFromSlots} - then tries \code{new(class)} and assigns slots of \code{object} to - the newly created instance. - - \code{getObjectSlots(object)} extracts the slot names and contents from - \code{object}. This is useful when \code{object} was created by a class - definition that is no longer current, and hence the contents of - \code{object} cannot be determined by accessing known slots. -} -\usage{ -updateObject(object, \dots, verbose=FALSE) -updateObjectTo(object, template, \dots, verbose=FALSE) -updateObjectFromSlots(object, objclass=class(object), \dots, verbose=FALSE) -getObjectSlots(object) -} -\arguments{ - \item{object}{Object to be updated, or for slot information to be - extracted from.} - \item{template}{Instance representing a template for updating object.} - \item{objclass}{Optional character string naming the class of the object to be created.} - \item{verbose}{A logical, indicating whether information about the - update should be reported. Use \code{message} to report this.} - \item{\dots}{Additional arguments, for use in specific update methods.} -} -\value{ - \code{updateObject} returns a valid instance of \code{object}. - \code{updateObjectTo} returns a valid instance of \code{template}. - \code{updateObjectFromSlots} returns an instance of class \code{objclass}. - \code{getObjectSlots} returns a list of named elements, with each - element corresponding to a slot in \code{object}. -} - -\author{Biocore team} - -\seealso{\code{\link{Versions-class}}} - -\examples{ -## update object, same class -data(sample.ExpressionSet) -obj <- updateObject(sample.ExpressionSet) - -setClass("UpdtA", representation(x="numeric"), contains="data.frame") -setMethod("updateObject", signature(object="UpdtA"), - function(object, ..., verbose=FALSE) { - if (verbose) message("updateObject object = 'A'") - object <- callNextMethod() - object@x <- -object@x - object -}) - -a <- new("UpdtA", x=1:10) -## See steps involved -updateObject(a) - -removeClass("UpdtA") -removeMethod("updateObject", "UpdtA") -} - -\keyword{manip} diff -Nru r-bioc-biobase-2.14.0/man/updateObjectTo.Rd r-bioc-biobase-2.20.0/man/updateObjectTo.Rd --- r-bioc-biobase-2.14.0/man/updateObjectTo.Rd 1970-01-01 00:00:00.000000000 +0000 +++ r-bioc-biobase-2.20.0/man/updateObjectTo.Rd 2013-04-03 22:22:31.000000000 +0000 @@ -0,0 +1,43 @@ +\name{updateObjectTo} +\alias{updateObjectTo} +\alias{updateObjectTo,ANY,ANY-method} + +\title{Update an object to the class definition of a template} +\description{ + The \code{updateObjectTo} generic function returns an instance + of \code{object} updated to the class definition of \code{template}. + + It requires that the class of the returned object be the same as the + class of the \code{template} argument, and that the object is valid. + Usually, updating proceeds by modifying slots in + \code{template} with information from \code{object}, and returning + \code{template}. Use \code{\link{as}} to coerce an object from one + type to another; \code{updateObjectTo} might be useful to update a + virtual superclass. By default, \code{updateObjectTo} has the following + behavior: + \describe{ + \item{\code{updateObjectTo(ANY-object,ANY-template)}}{Attempt \code{as(ANY-object,class(ANY-template))}.} + } +} +\usage{ +updateObjectTo(object, template, \dots, verbose=FALSE) +} +\arguments{ + \item{object}{Object to be updated.} + \item{template}{Instance representing a template for updating object.} + \item{\dots}{Additional arguments, for use in specific update methods.} + \item{verbose}{A logical, indicating whether information about the + update should be reported. Use \code{message} to report this.} +} +\value{ + \code{updateObjectTo} returns a valid instance of \code{template}. +} + +\author{Biocore team} + +\seealso{ + \code{\link[BiocGenerics]{updateObject}}, + \code{\link{Versions-class}} +} + +\keyword{manip} diff -Nru r-bioc-biobase-2.14.0/src/Rinit.c r-bioc-biobase-2.20.0/src/Rinit.c --- r-bioc-biobase-2.14.0/src/Rinit.c 2011-11-01 04:27:52.000000000 +0000 +++ r-bioc-biobase-2.20.0/src/Rinit.c 2013-04-04 06:39:20.000000000 +0000 @@ -1,6 +1,5 @@ #include #include -#include #include SEXP anyMissing(SEXP); diff -Nru r-bioc-biobase-2.14.0/src/envir.c r-bioc-biobase-2.20.0/src/envir.c --- r-bioc-biobase-2.14.0/src/envir.c 2011-11-01 04:27:52.000000000 +0000 +++ r-bioc-biobase-2.20.0/src/envir.c 2013-04-04 06:39:20.000000000 +0000 @@ -2,7 +2,6 @@ #include #include -#include #include #include /* diff -Nru r-bioc-biobase-2.14.0/tests/test-all.R r-bioc-biobase-2.20.0/tests/test-all.R --- r-bioc-biobase-2.14.0/tests/test-all.R 1970-01-01 00:00:00.000000000 +0000 +++ r-bioc-biobase-2.20.0/tests/test-all.R 2013-04-03 22:22:27.000000000 +0000 @@ -0,0 +1,2 @@ +require("Biobase") || stop("unable to load Biobase") +BiocGenerics:::testPackage("Biobase", "UnitTests", ".*_test\\.R$")