BioC 2.12: CHECK report for marray on pelham

Package: marray

Version: 1.38.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch marray_1.38.0.tar.gz

StartedAt: 2013-05-01 07:40:26 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 07:42:49 -0700 (Wed, 01 May 2013)

EllapsedTime: 143.0 seconds

RetCode: 0

Status: OK

CheckDir: marray.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/marray.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'marray/DESCRIPTION' ... OK
* this is package 'marray' version '1.38.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'marray' can be installed ... [7s/11s] OK
* checking installed package size ... NOTE
  installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc         1.6Mb
    swirldata   5.5Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* checking for left-over 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 package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... 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 ... NOTE
maImage: warning in layout(matrix(c(1, 2), 1, 2), width = c(8, 2)):
  partial argument match of 'width' to 'widths'
widget.marrayInfo : inputInfo: warning in assign(newname, newInfo, env
  = .GlobalEnv): partial argument match of 'env' to 'envir'
widget.marrayLayout : inputLayout: warning in assign(newname,
  newLayout, env = .GlobalEnv): partial argument match of 'env' to
  'envir'
widget.marrayRaw : inputRaw: warning in assign(newname, newRaw, env =
  .GlobalEnv): partial argument match of 'env' to 'envir'
maA,marrayRaw: warning in matrix(nr = 0, nc = 0): partial argument
  match of 'nr' to 'nrow'
maA,marrayRaw: warning in matrix(nr = 0, nc = 0): partial argument
  match of 'nc' to 'ncol'
maM,marrayRaw: warning in matrix(nr = 0, nc = 0): partial argument
  match of 'nr' to 'nrow'
maM,marrayRaw: warning in matrix(nr = 0, nc = 0): partial argument
  match of 'nc' to 'ncol'
findID: no visible binding for global variable 'gnames'
findID: no visible global function definition for 'phenoData'
htmlPage: no visible binding for global variable 'Gnames'
maTwoSamples: no visible global function definition for 'gpTools'
scale.na: no visible global function definition for 'applyy'
widget.TwoSamples: no visible global function definition for
  'widgetRender'
widget.mapGeneInfo: no visible global function definition for
  'widgetRender'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [58s/59s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
maNormMain     26.585  0.192  27.172
read.marrayRaw  5.730  0.097   5.910
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 3 notes.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/marray.Rcheck/00check.log'
for details.

* installing *source* package 'marray' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (marray)

name	user	system	elapsed
boxplot	1.185	0.069	1.388
checkTargetInfo	0.242	0.022	0.275
dim	0.094	0.002	0.097
findID	0.123	0.017	0.140
htmlPage	0.196	0.027	0.225
image	0.099	0.012	0.120
ma2D	0.012	0.001	0.014
maBoxplot	0.007	0.000	0.008
maColorBar	0.054	0.004	0.062
maCompCoord	0.012	0.004	0.017
maCompInd	0.017	0.003	0.020
maCompLayout	0.022	0.002	0.024
maCompNormA	0.008	0.001	0.011
maCompPlate	0.034	0.002	0.038
maCoord2Ind	0.016	0.005	0.022
maDefaultPar	0.011	0.003	0.013
maDotsDefaults	0.023	0.006	0.030
maDotsMatch	0.011	0.003	0.015
maGenControls	0.271	0.021	0.294
maGeneTable	0.190	0.021	0.213
maImage	1.843	0.057	1.948
maImage.func	0.006	0.003	0.008
maInd2Coord	0.011	0.003	0.016
maLegendLines	0.007	0.001	0.008
maLoess	0.006	0.001	0.006
maLoessLines	0.008	0.001	0.008
maMAD	0.096	0.002	0.098
maMed	0.006	0.003	0.009
maNorm	3.979	0.054	4.156
maNorm2D	0.013	0.001	0.014
maNormLoess	0.094	0.004	0.100
maNormMAD	0.004	0.004	0.009
maNormMain	26.585	0.192	27.172
maNormMed	0.006	0.000	0.007
maNormScale	0.792	0.034	0.836
maNum2Logic	0.010	0.004	0.014
maPalette	0.052	0.008	0.067
maPlot	4.265	0.086	4.498
maPlot.func	0.008	0.001	0.008
maSelectGnames	0.022	0.001	0.023
maText	0.009	0.001	0.010
maTop	0.007	0.000	0.008
mapGeneInfo	0.011	0.001	0.012
marrayInfo-class	0.013	0.001	0.013
marrayLayout-class	0.008	0.008	0.016
marrayNorm-class	0.678	0.053	0.745
marrayRaw-class	0.256	0.032	0.293
opVersionID	0.086	0.002	0.089
plotMA	3.938	0.069	4.071
read.Galfile	0.116	0.008	0.129
read.marrayInfo	0.128	0.007	0.134
read.marrayLayout	0.256	0.007	0.263
read.marrayRaw	5.730	0.097	5.910
rm.na	0.008	0.006	0.013
stat.confband.text	0.884	0.065	0.961
stat.gnames	0.539	0.040	0.579
write.list	0.327	0.036	0.364
write.marray	0.123	0.020	0.147
write.xls	0.177	0.044	0.223

Summary

Command output