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IMPORTANT NOTE: R was configured with --enable-strict-barrier on lamb1 |
Package 195/247 | Hostname | OS | Arch | BUILD | CHECK | BUILD BIN |
rflowcyt1.9.1N. LeMeurLast Changed Date: 2007-05-15 20:29:38 -0700 Last Changed Rev: 24690 | lamb1 | Linux (SUSE 10.1) | x86_64 | OK | ERROR | |
wellington | Linux (SUSE 9.2) | i686 | OK | [ ERROR ] | ||
liverpool | Windows Server 2003 R2 (32-bit) | x64 | OK | ERROR | OK | |
pitt | Mac OS X (10.4.10) | i386 | OK | ERROR | OK |
Package: rflowcyt |
Version: 1.9.1 |
Command: /loc/biocbuild/bbs-2.1-bioc/R/bin/R CMD check rflowcyt_1.9.1.tar.gz |
RetCode: 1 |
Time: 271.8 seconds |
Status: ERROR |
CheckDir: rflowcyt.Rcheck |
Warnings: NA |
* checking for working latex ... OK * using log directory '/extra/loc/biocbuild/bbs-2.1-bioc/meat/rflowcyt.Rcheck' * using R version 2.6.0 Under development (unstable) (2007-08-06 r42439) * checking for file 'rflowcyt/DESCRIPTION' ... OK * this is package 'rflowcyt' version '1.9.1' * checking package name space information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking whether package 'rflowcyt' can be installed ... OK * checking package directory ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the name space can be loaded with stated dependencies ... OK * checking for unstated dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented S4 methods: generic '[[<-' and siglist 'FCS,ANY,ANY' generic '[[<-' and siglist 'FCSmetadata,ANY,ANY' All user-level objects in a package (including S4 classes and methods) should have documentation entries. See the chapter 'Writing R documentation files' in manual 'Writing R Extensions'. * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * creating rflowcyt-Ex.R ... OK * checking examples ... ERROR Running examples in 'rflowcyt-Ex.R' failed. The error most likely occurred in: > ### * cytoSet-class > > flush(stderr()); flush(stdout()) > > ### Name: cytoSet-class > ### Title: 'cytoSet': a class for storing raw data from a quantitative > ### cell-based assay > ### Aliases: cytoSet-class [,cytoSet-method [[,cytoSet-method > ### [[<-,cytoSet-method show,cytoSet-method length,cytoSet-method > ### pData,cytoSet-method colnames,cytoSet-method > ### colnames<-,cytoSet-method phenoData,cytoSet-method > ### phenoData<-,cytoSet,phenoData-method > ### Keywords: classes > > ### ** Examples > > if (require(prada)) { + cset<-readCytoSet(path=system.file("extdata", package="prada"), + pattern="[A-Z][0-9][0-9]$") + cset + pData(cset) + cset[[1]] + cset[["fas-Bcl2-plate323-04-04.A02"]] + cset["fas-Bcl2-plate323-04-04.A02"] + cset[1:3] + cset[[1]] <- exprs(cset[[1]])[1:100, ] + + plot(cset[[2]]) + } Error in function (classes, fdef, mtable) : unable to find an inherited method for function "pData<-", for signature "AnnotatedDataFrame", "AsIs" Calls: [ -> [ -> pData<- -> <Anonymous> Execution halted
rflowcyt.Rcheck/00install.out:
* Installing *source* package 'rflowcyt' ... ** R ** inst ** preparing package for lazy loading Loading required package: survival Loading required package: splines Loading required package: xtable Loading required package: KernSmooth KernSmooth 2.22 installed Copyright M. P. Wand 1997 Loading required package: MASS Loading required package: grid Loading required package: hexbin Loading required package: lattice Loading required package: rfcdmin Loading required package: fields fields is loaded use help(fields) for an overview of this library Some name changes have been made to several common functions: exp.-> Exp. and rad. -> Rad. See help( Exp.cov) Loading required package: locfit Loading required package: akima locfit 1.5-3 2006-04-06 Loading required package: splancs Loading required package: sp Spatial Point Pattern Analysis Code in S-Plus Version 2 - Spatial and Space-Time analysis Loading required package: prada Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. Loading required package: RColorBrewer Scalable Robust Estimators with High Breakdown Point (version 0.3-06) Loading required package: xgobi Creating a new generic function for "print" in "rflowcyt" ** help >>> Building/Updating help pages for package 'rflowcyt' Formats: text html latex example ContourScatterPlot text html latex example FCS-class text html latex example FCSgate-class text html latex example FCSggobi-class text html latex example FCSmetadata-class text html latex example FCSsummary-class text html latex example FHCRC.HVTNFCS text html latex example ImageParCoord text html latex example KS.flowcytest text html latex example MODE text html latex example PercentPos.FCS text html latex example ProbBin.FCS text html latex example ProbBin.flowcytest text html latex example ROC.FCS text html latex example VRC.HVTNFCS text html latex example WLR.flowcytest text html latex example add.parallel.coordinates text html latex example add.parallelCoordinates text html latex example addParameter-methods text html latex boxplot.FCS text html latex example breakpoints.ProbBin text html latex example checkvars-methods text html latex coerce-FCSformat text html latex example coerce-methods text html latex convertS3toS4 text html latex example createGate text html latex example cytoSet-class text html latex example dim.FCS-methods text html latex emp.f text html latex example equals-methods text html latex extractGateHistory text html latex example extractGatedData text html latex example fcs.type text html latex example fixvars-methods text html latex fluors-methods text html latex gate.IPC text html latex example get.h text html latex example get.num.modes text html latex example get.p text html latex example ggobi-methods text html latex legend.CSP text html latex example make.grid text html latex example metaData-methods text html latex pairs.CSP text html latex example parallelCoordinates text html latex example pkci2.flowcytest text html latex example plot-methods text html latex plot.ProbBin.FCS text html latex example plot2sets.FCS text html latex example plotECDF.FCS text html latex example plotQA.FCS text html latex example plotdensity.FCS text html latex example plotvar.FCS text html latex example print-methods text html latex read.FCS text html latex example read.series.FCS text html latex example rect.box.idx text html latex example rflowcyt-defunct text html latex runflowcytests text html latex example show-methods text html latex showgate.FCS text html latex example standard text html latex example subset-methods text html latex subset2-methods text html latex subset2assign-methods text html latex subsetassign-methods text html latex summary-methods text html latex summary.ProbBin.FCS text html latex example xgobi.FCS text html latex example ** building package indices ... * DONE (rflowcyt)