BioC 2.13: CHECK report for marray on perceval

Package: marray

Version: 1.40.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch marray_1.40.0.tar.gz

StartedAt: 2014-04-05 02:25:48 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 02:27:40 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 111.5 seconds

RetCode: 0

Status:  OK

CheckDir: marray.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/marray.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘marray/DESCRIPTION’ ... OK
* this is package ‘marray’ version ‘1.40.0’
* 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 ... [6s/7s] 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 ‘build’ 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 dependencies in R code ... NOTE
Package in Depends field not imported from: ‘limma’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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.mapGeneInfo: no visible global function definition for
  ‘widgetRender’
widget.TwoSamples: 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘marray.Rnw’, ‘marrayClasses.Rnw’, ‘marrayClassesShort.Rnw’,
  ‘marrayInput.Rnw’, ‘marrayNorm.Rnw’, ‘marrayPlots.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [38s/39s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
maNormMain 15.414  0.143  15.946
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 5 notes.
See
  ‘/Users/biocbuild/bbs-2.13-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	1.121	0.053	1.215
checkTargetInfo	0.317	0.019	0.347
dim	0.013	0.002	0.017
findID	0.113	0.012	0.129
htmlPage	0.199	0.018	0.217
image	0.081	0.013	0.094
ma2D	0.011	0.001	0.012
maBoxplot	0.007	0.001	0.007
maColorBar	0.046	0.004	0.053
maCompCoord	0.013	0.001	0.013
maCompInd	0.018	0.001	0.018
maCompLayout	0.028	0.002	0.029
maCompNormA	0.007	0.000	0.008
maCompPlate	0.021	0.001	0.022
maCoord2Ind	0.106	0.002	0.107
maDefaultPar	0.005	0.003	0.007
maDotsDefaults	0.011	0.003	0.014
maDotsMatch	0.006	0.002	0.009
maGenControls	0.236	0.012	0.252
maGeneTable	0.093	0.028	0.123
maImage	1.561	0.072	1.666
maImage.func	0.007	0.001	0.008
maInd2Coord	0.013	0.001	0.013
maLegendLines	0.005	0.000	0.006
maLoess	0.003	0.003	0.006
maLoessLines	0.004	0.002	0.005
maMAD	0.004	0.003	0.007
maMed	0.004	0.002	0.006
maNorm	2.444	0.042	2.536
maNorm2D	0.009	0.001	0.010
maNormLoess	0.007	0.001	0.007
maNormMAD	0.006	0.000	0.007
maNormMain	15.414	0.143	15.946
maNormMed	0.01	0.00	0.01
maNormScale	0.577	0.037	0.623
maNum2Logic	0.009	0.001	0.012
maPalette	0.126	0.008	0.140
maPlot	2.658	0.093	2.798
maPlot.func	0.005	0.001	0.006
maSelectGnames	0.018	0.002	0.020
maText	0.004	0.001	0.006
maTop	0.005	0.001	0.007
mapGeneInfo	0.008	0.001	0.010
marrayInfo-class	0.011	0.002	0.013
marrayLayout-class	0.017	0.004	0.020
marrayNorm-class	0.634	0.048	0.690
marrayRaw-class	0.273	0.025	0.306
opVersionID	0.008	0.003	0.011
plotMA	2.290	0.059	2.384
read.Galfile	0.140	0.004	0.144
read.marrayInfo	0.144	0.003	0.152
read.marrayLayout	0.346	0.007	0.354
read.marrayRaw	3.746	0.105	3.879
rm.na	0.009	0.003	0.012
stat.confband.text	0.739	0.054	0.810
stat.gnames	0.467	0.053	0.532
write.list	0.199	0.059	0.263
write.marray	0.110	0.033	0.146
write.xls	0.126	0.037	0.181