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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: E:\biocbld\bbs-2.1-bioc\R\bin\R.exe CMD check rflowcyt_1.9.1.tar.gz |
RetCode: 1 |
Time: 108.4 seconds |
Status: ERROR |
CheckDir: rflowcyt.Rcheck |
Warnings: NA |
* checking for working latex ... OK * using log directory 'E:/biocbld/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 ... WARNING Found the following significant warnings: missing link(s): xyplot missing link(s): xyplot xyplot xyplot lattice lattice xyplot See 'E:/biocbld/bbs-2.1-bioc/meat/rflowcyt.Rcheck/00install.out' for details. * checking package directory ... OK * checking for portable file names ... 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 R.css in E:/biocbld/bbs-2.1-bioc/meat/rflowcyt.Rcheck ---------- Making package rflowcyt ------------ adding build stamp to DESCRIPTION installing NAMESPACE file and metadata installing R files installing inst files installing man source files installing indices installing help >>> Building/Updating help pages for package 'rflowcyt' Formats: text html latex example chm ContourScatterPlot text html latex example chm FCS-class text html latex example chm FCSgate-class text html latex example chm FCSggobi-class text html latex example chm FCSmetadata-class text html latex example chm FCSsummary-class text html latex example chm FHCRC.HVTNFCS text html latex example chm ImageParCoord text html latex example chm KS.flowcytest text html latex example chm MODE text html latex example chm PercentPos.FCS text html latex example chm ProbBin.FCS text html latex example chm ProbBin.flowcytest text html latex example chm ROC.FCS text html latex example chm VRC.HVTNFCS text html latex example chm WLR.flowcytest text html latex example chm add.parallel.coordinates text html latex example chm add.parallelCoordinates text html latex example chm addParameter-methods text html latex chm boxplot.FCS text html latex example chm missing link(s): xyplot breakpoints.ProbBin text html latex example chm checkvars-methods text html latex chm coerce-FCSformat text html latex example chm coerce-methods text html latex chm convertS3toS4 text html latex example chm createGate text html latex example chm cytoSet-class text html latex example chm dim.FCS-methods text html latex chm emp.f text html latex example chm equals-methods text html latex chm extractGateHistory text html latex example chm extractGatedData text html latex example chm fcs.type text html latex example chm fixvars-methods text html latex chm fluors-methods text html latex chm gate.IPC text html latex example chm get.h text html latex example chm get.num.modes text html latex example chm get.p text html latex example chm ggobi-methods text html latex chm legend.CSP text html latex example chm make.grid text html latex example chm metaData-methods text html latex chm pairs.CSP text html latex example chm parallelCoordinates text html latex example chm pkci2.flowcytest text html latex example chm plot-methods text html latex chm plot.ProbBin.FCS text html latex example chm plot2sets.FCS text html latex example chm plotECDF.FCS text html latex example chm missing link(s): xyplot xyplot xyplot lattice lattice xyplot plotQA.FCS text html latex example chm plotdensity.FCS text html latex example chm plotvar.FCS text html latex example chm print-methods text html latex chm read.FCS text html latex example chm read.series.FCS text html latex example chm rect.box.idx text html latex example chm rflowcyt-defunct text html latex chm runflowcytests text html latex example chm show-methods text html latex chm showgate.FCS text html latex example chm standard text html latex example chm subset-methods text html latex chm subset2-methods text html latex chm subset2assign-methods text html latex chm subsetassign-methods text html latex chm summary-methods text html latex chm summary.ProbBin.FCS text html latex example chm xgobi.FCS text html latex example chm Microsoft HTML Help Compiler 4.74.8702 Compiling e:\biocbld\bbs-2.1-bioc\meat\rflowcyt.Rcheck\00_pkg_src\rflowcyt\chm\rflowcyt.chm Compile time: 0 minutes, 1 second 70 Topics 560 Local links 1 Internet link 1 Graphic Created e:\biocbld\bbs-2.1-bioc\meat\rflowcyt.Rcheck\00_pkg_src\rflowcyt\chm\rflowcyt.chm, 174,197 bytes Compression decreased file by 287,860 bytes. preparing package rflowcyt 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 Loading required package: locfit Loading required package: akima Loading required package: splancs Loading required package: sp 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 Loading required package: xgobi Creating a new generic function for "print" in "rflowcyt" adding MD5 sums * DONE (rflowcyt)