CHECK report for marray on lemming

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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: D:\biocbld\1.9d\R\bin\R.exe CMD check marray_1.12.0.tar.gz

RetCode: 0

Time: 238.4 seconds

Status: WARNINGS

CheckDir: marray.Rcheck

Warnings: 1

Command output

* checking for working latex ... OK
* using log directory 'D:/biocbld/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 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
  D:/biocbld/1.9d/Rpacks/marray.Rcheck/00check.log
for details

marray.Rcheck/00install.out:

installing R.css in D:/biocbld/1.9d/Rpacks/marray.Rcheck


---------- Making package marray ------------
  adding build stamp to DESCRIPTION
  installing R files
  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"
  installing inst files
  installing data files
  installing man source files
  installing indices
  not zipping data
  installing help
 >>> Building/Updating help pages for package 'marray'
     Formats: text html latex example chm 
  boxplot                           text    html    latex   example chm
  bracketMethods                    text    html    latex           chm
  cbind                             text    html    latex   example chm
  checkTargetInfo                   text    html    latex   example chm
  coerce-methods                    text    html    latex           chm
  dim                               text    html    latex   example chm
  findID                            text    html    latex   example chm
  htmlPage                          text    html    latex   example chm
  image                             text    html    latex   example chm
  ma2D                              text    html    latex   example chm
  maBoxplot                         text    html    latex   example chm
  maColorBar                        text    html    latex   example chm
  maCompCoord                       text    html    latex   example chm
  maCompInd                         text    html    latex   example chm
  maCompLayout                      text    html    latex   example chm
  maCompNormA                       text    html    latex   example chm
  maCompPlate                       text    html    latex   example chm
  maCoord2Ind                       text    html    latex   example chm
  maDefaultPar                      text    html    latex   example chm
  maDotsDefaults                    text    html    latex   example chm
  maDotsMatch                       text    html    latex   example chm
  maGenControls                     text    html    latex   example chm
  maGeneTable                       text    html    latex   example chm
  maImage                           text    html    latex   example chm
  maImage.func                      text    html    latex   example chm
  maInd2Coord                       text    html    latex   example chm
  maLegendLines                     text    html    latex   example chm
  maLoess                           text    html    latex   example chm
  maLoessLines                      text    html    latex   example chm
  maMAD                             text    html    latex   example chm
  maMed                             text    html    latex   example chm
  maNA                              text    html    latex           chm
  maNorm                            text    html    latex   example chm
  maNorm2D                          text    html    latex   example chm
  maNormLoess                       text    html    latex   example chm
  maNormMAD                         text    html    latex   example chm
  maNormMain                        text    html    latex   example chm
  maNormMed                         text    html    latex   example chm
  maNormScale                       text    html    latex   example chm
  maNum2Logic                       text    html    latex   example chm
  maPalette                         text    html    latex   example chm
  maPlot                            text    html    latex   example chm
  maPlot.func                       text    html    latex   example chm
  maSelectGnames                    text    html    latex   example chm
  maText                            text    html    latex   example chm
  maTop                             text    html    latex   example chm
  maTwoSamples                      text    html    latex           chm
  mapGeneInfo                       text    html    latex   example chm
  marray-internal                   text    html    latex           chm
  marrayInfo-class                  text    html    latex   example chm
  marrayLayout-class                text    html    latex   example chm
  marrayNorm-class                  text    html    latex   example chm
  marrayRaw-class                   text    html    latex   example chm
  opVersionID                       text    html    latex   example chm
  plotMA                            text    html    latex   example chm
  print-methods                     text    html    latex           chm
  read.Galfile                      text    html    latex   example chm
  read.marrayInfo                   text    html    latex   example chm
  read.marrayLayout                 text    html    latex   example chm
  read.marrayRaw                    text    html    latex   example chm
  rm.na                             text    html    latex   example chm
  showLargeObject                   text    html    latex   example chm
  stat.confband.text                text    html    latex   example chm
  stat.gnames                       text    html    latex   example chm
  swirl                             text    html    latex           chm
  write.list                        text    html    latex   example chm
  write.marray                      text    html    latex   example chm
  write.xls                         text    html    latex   example chm
Microsoft HTML Help Compiler 4.74.8702

Compiling d:\biocbld\1.9d\Rpacks\marray.Rcheck\00_pkg_src\marray\chm\marray.chm


Compile time: 0 minutes, 0 seconds
69	Topics
700	Local links
37	Internet links
1	Graphic


Created d:\biocbld\1.9d\Rpacks\marray.Rcheck\00_pkg_src\marray\chm\marray.chm, 109,607 bytes
Compression decreased file by 270,284 bytes.
  adding MD5 sums

* DONE (marray)