CHECK report for marray on churchill

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Package 105/188	OS	Arch	BUILD	CHECK	BUILD BIN
marray 1.12.0 Yee Hwa (Jean) Yang	Linux (SUSE 9.2)	x86_64	OK	WARNINGS
	Linux (SUSE 9.2)	i686	OK	WARNINGS
	Solaris 2.9	sparc	OK	[ WARNINGS ]
	Windows Server 2003	x86_64	OK	WARNINGS	OK

Package: marray

Version: 1.12.0

Command: /loc/biocbuild/1.9d/R/bin/R CMD check marray_1.12.0.tar.gz

RetCode: 0

Time: 602.8 seconds

Status: WARNINGS

CheckDir: marray.Rcheck

Warnings: 1

Command output

* checking for working latex ... OK
* using log directory '/loc/biocbuild/1.9d/Rpacks/marray.Rcheck'
* using R version 2.4.0 (2006-10-03)
* checking for file 'marray/DESCRIPTION' ... OK
* this is package 'marray' version '1.12.0'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'marray' 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 syntax errors ... OK
* checking R files for non-ASCII characters ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... 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 'maSub<-' and siglist 'marrayRaw,ANY'
  generic 'maSub<-' and siglist 'marrayNorm,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 marray-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating marray-manual.tex ... OK
* checking marray-manual.tex ... OK

WARNING: There was 1 warning, see
  /loc/biocbuild/1.9d/Rpacks/marray.Rcheck/00check.log
for details

marray.Rcheck/00install.out:

* Installing *source* package 'marray' ...
** R
** data
** inst
** save image
Loading required package: limma
[1] "marrayInfo"
[1] "marrayLayout"
[1] "marrayRaw"
[1] "marrayNorm"
[1] "maLabels"
[1] "maLabels"
[1] "maInfo"
[1] "maInfo"
[1] "maNotes"
[1] "maNotes"
[1] "maNspots"
[1] "maNspots"
[1] "maNgr"
[1] "maNgr"
[1] "maNgc"
[1] "maNgc"
[1] "maNsr"
[1] "maNsr"
[1] "maNsc"
[1] "maNsc"
[1] "maSub"
[1] "maSub"
[1] "maPlate"
[1] "maPlate"
[1] "maControls"
[1] "maControls"
[1] "maNotes"
[1] "maGridRow"
[1] "maGridRow"
[1] "maGridCol"
[1] "maGridCol"
[1] "maSpotRow"
[1] "maSpotRow"
[1] "maSpotCol"
[1] "maSpotCol"
[1] "maPrintTip"
[1] "maPrintTip"
[1] "maRf"
[1] "maRf"
[1] "maGf"
[1] "maGf"
[1] "maRb"
[1] "maRb"
[1] "maGb"
[1] "maGb"
[1] "maW"
[1] "maW"
[1] "maLR"
[1] "maLR"
[1] "maLG"
[1] "maLG"
[1] "maM"
[1] "maM"
[1] "maA"
[1] "maA"
[1] "maLayout"
[1] "maLayout"
[1] "maNspots"
[1] "maNgr"
[1] "maNgc"
[1] "maNsr"
[1] "maNsc"
[1] "maGridRow"
[1] "maGridCol"
[1] "maSpotRow"
[1] "maSpotCol"
[1] "maPrintTip"
[1] "maSub"
[1] "maPlate"
[1] "maControls"
[1] "maNsamples"
[1] "maNsamples"
[1] "maGnames"
[1] "maGnames"
[1] "maTargets"
[1] "maTargets"
[1] "maNotes"
[1] "maA"
[1] "maM"
[1] "maMloc"
[1] "maMloc"
[1] "maMscale"
[1] "maMscale"
[1] "maW"
[1] "maLR"
[1] "maLG"
[1] "maLayout"
[1] "maNspots"
[1] "maNgr"
[1] "maNgc"
[1] "maNsr"
[1] "maNsc"
[1] "maGridRow"
[1] "maGridCol"
[1] "maSpotRow"
[1] "maSpotCol"
[1] "maPrintTip"
[1] "maSub"
[1] "maPlate"
[1] "maControls"
[1] "maNsamples"
[1] "maGnames"
[1] "maTargets"
[1] "maNotes"
[1] "maNormCall"
[1] "maNormCall"
[1] "maLabels<-"
[1] "maLabels<-"
[1] "maLabels<-"
[1] "maInfo<-"
[1] "maInfo<-"
[1] "maNgr<-"
[1] "maNgr<-"
[1] "maNgr<-"
[1] "maNgr<-"
[1] "maNgc<-"
[1] "maNgc<-"
[1] "maNgc<-"
[1] "maNgc<-"
[1] "maNsr<-"
[1] "maNsr<-"
[1] "maNsr<-"
[1] "maNsr<-"
[1] "maNsc<-"
[1] "maNsc<-"
[1] "maNsc<-"
[1] "maNsc<-"
[1] "maNspots<-"
[1] "maNspots<-"
[1] "maNspots<-"
[1] "maNspots<-"
[1] "maSub<-"
[1] "maSub<-"
[1] "maSub<-"
[1] "maSub<-"
[1] "maSub<-"
[1] "maPlate<-"
[1] "maPlate<-"
[1] "maPlate<-"
[1] "maPlate<-"
[1] "maControls<-"
[1] "maControls<-"
[1] "maControls<-"
[1] "maControls<-"
[1] "maLayout<-"
[1] "maLayout<-"
[1] "maLayout<-"
[1] "maGnames<-"
[1] "maGnames<-"
[1] "maGnames<-"
[1] "maTargets<-"
[1] "maTargets<-"
[1] "maTargets<-"
[1] "maW<-"
[1] "maW<-"
[1] "maW<-"
[1] "maGf<-"
[1] "maGf<-"
[1] "maRf<-"
[1] "maRf<-"
[1] "maGb<-"
[1] "maGb<-"
[1] "maGb<-"
[1] "maRb<-"
[1] "maRb<-"
[1] "maRb<-"
[1] "maA<-"
[1] "maA<-"
[1] "maM<-"
[1] "maM<-"
[1] "maMloc<-"
[1] "maMloc<-"
[1] "maMscale<-"
[1] "maMscale<-"
[1] "maNotes<-"
[1] "maNotes<-"
[1] "maNotes<-"
[1] "maNotes<-"
[1] "maNotes<-"
[1] "summary"
[1] "summary"
[1] "summary"
[1] "summary"
[1] "summary"
[1] "ShowLargeObject"
[1] "show"
[1] "["
[1] "["
[1] "["
[1] "["
[1] "boxplot"
[1] "boxplot"
[1] "boxplot"
[1] "image"
[1] "image"
[1] "image"
[1] "points"
[1] "points"
[1] "points"
[1] "text"
[1] "text"
[1] "text"
[1] "lines"
[1] "lines"
[1] "lines"
** help
 >>> Building/Updating help pages for package 'marray'
     Formats: text html latex example 
  boxplot                           text    html    latex   example
  bracketMethods                    text    html    latex
  cbind                             text    html    latex   example
  checkTargetInfo                   text    html    latex   example
  coerce-methods                    text    html    latex
  dim                               text    html    latex   example
  findID                            text    html    latex   example
  htmlPage                          text    html    latex   example
  image                             text    html    latex   example
  ma2D                              text    html    latex   example
  maBoxplot                         text    html    latex   example
  maColorBar                        text    html    latex   example
  maCompCoord                       text    html    latex   example
  maCompInd                         text    html    latex   example
  maCompLayout                      text    html    latex   example
  maCompNormA                       text    html    latex   example
  maCompPlate                       text    html    latex   example
  maCoord2Ind                       text    html    latex   example
  maDefaultPar                      text    html    latex   example
  maDotsDefaults                    text    html    latex   example
  maDotsMatch                       text    html    latex   example
  maGenControls                     text    html    latex   example
  maGeneTable                       text    html    latex   example
  maImage                           text    html    latex   example
  maImage.func                      text    html    latex   example
  maInd2Coord                       text    html    latex   example
  maLegendLines                     text    html    latex   example
  maLoess                           text    html    latex   example
  maLoessLines                      text    html    latex   example
  maMAD                             text    html    latex   example
  maMed                             text    html    latex   example
  maNA                              text    html    latex
  maNorm                            text    html    latex   example
  maNorm2D                          text    html    latex   example
  maNormLoess                       text    html    latex   example
  maNormMAD                         text    html    latex   example
  maNormMain                        text    html    latex   example
  maNormMed                         text    html    latex   example
  maNormScale                       text    html    latex   example
  maNum2Logic                       text    html    latex   example
  maPalette                         text    html    latex   example
  maPlot                            text    html    latex   example
  maPlot.func                       text    html    latex   example
  maSelectGnames                    text    html    latex   example
  maText                            text    html    latex   example
  maTop                             text    html    latex   example
  maTwoSamples                      text    html    latex
  mapGeneInfo                       text    html    latex   example
  marray-internal                   text    html    latex
  marrayInfo-class                  text    html    latex   example
  marrayLayout-class                text    html    latex   example
  marrayNorm-class                  text    html    latex   example
  marrayRaw-class                   text    html    latex   example
  opVersionID                       text    html    latex   example
  plotMA                            text    html    latex   example
  print-methods                     text    html    latex
  read.Galfile                      text    html    latex   example
  read.marrayInfo                   text    html    latex   example
  read.marrayLayout                 text    html    latex   example
  read.marrayRaw                    text    html    latex   example
  rm.na                             text    html    latex   example
  showLargeObject                   text    html    latex   example
  stat.confband.text                text    html    latex   example
  stat.gnames                       text    html    latex   example
  swirl                             text    html    latex
  write.list                        text    html    latex   example
  write.marray                      text    html    latex   example
  write.xls                         text    html    latex   example
** building package indices ...
* DONE (marray)