BioC 2.12: CHECK report for marray on petty

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: 2013-10-08 22:59:29 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 23:01:55 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 145.5 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 3.0.1 (2013-05-16)
* 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 ... [8s/8s] 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [52s/53s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
maNormMain     22.479  0.159  22.825
read.marrayRaw  6.080  0.087   6.263
* 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	1.072	0.057	1.147
checkTargetInfo	0.248	0.027	0.280
dim	0.092	0.002	0.093
findID	0.138	0.014	0.152
htmlPage	0.190	0.026	0.220
image	0.112	0.022	0.135
ma2D	0.005	0.000	0.005
maBoxplot	0.005	0.001	0.007
maColorBar	0.045	0.003	0.049
maCompCoord	0.010	0.002	0.012
maCompInd	0.014	0.002	0.017
maCompLayout	0.017	0.001	0.018
maCompNormA	0.010	0.001	0.012
maCompPlate	0.028	0.002	0.031
maCoord2Ind	0.018	0.002	0.020
maDefaultPar	0.005	0.002	0.007
maDotsDefaults	0.011	0.003	0.015
maDotsMatch	0.009	0.003	0.013
maGenControls	0.345	0.024	0.371
maGeneTable	0.196	0.014	0.214
maImage	1.696	0.091	1.848
maImage.func	0.007	0.000	0.007
maInd2Coord	0.021	0.001	0.023
maLegendLines	0.009	0.000	0.010
maLoess	0.009	0.000	0.009
maLoessLines	0.008	0.000	0.008
maMAD	0.007	0.001	0.008
maMed	0.01	0.00	0.01
maNorm	3.510	0.048	3.581
maNorm2D	0.009	0.001	0.011
maNormLoess	0.009	0.000	0.008
maNormMAD	0.008	0.001	0.009
maNormMain	22.479	0.159	22.825
maNormMed	0.009	0.001	0.010
maNormScale	0.650	0.048	0.707
maNum2Logic	0.009	0.000	0.010
maPalette	0.062	0.004	0.070
maPlot	3.813	0.081	3.939
maPlot.func	0.008	0.001	0.009
maSelectGnames	0.101	0.003	0.104
maText	0.002	0.002	0.004
maTop	0.005	0.003	0.008
mapGeneInfo	0.004	0.004	0.008
marrayInfo-class	0.006	0.006	0.011
marrayLayout-class	0.009	0.007	0.016
marrayNorm-class	0.652	0.053	0.836
marrayRaw-class	0.240	0.030	0.271
opVersionID	0.01	0.00	0.01
plotMA	3.437	0.060	3.539
read.Galfile	0.127	0.005	0.133
read.marrayInfo	0.154	0.004	0.165
read.marrayLayout	0.289	0.006	0.301
read.marrayRaw	6.080	0.087	6.263
rm.na	0.012	0.005	0.018
stat.confband.text	1.082	0.044	1.188
stat.gnames	0.630	0.042	0.705
write.list	0.232	0.048	0.281
write.marray	0.141	0.019	0.161
write.xls	0.180	0.038	0.221