BioC 2.13: CHECK report for marray on zin1

Package: marray

Version: 1.40.0

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings marray_1.40.0.tar.gz

StartedAt: 2014-04-05 02:14:19 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 02:15:30 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 70.9 seconds

RetCode: 0

Status:  OK

CheckDir: marray.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/marray.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (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 ... [4s/4s] OK
* checking installed package size ... NOTE
  installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc         1.7Mb
    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.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 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 ... [27s/27s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
maNormMain 12.877  0.004  12.903
* 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
  ‘/home/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	0.568	0.000	0.567
checkTargetInfo	0.132	0.004	0.139
dim	0.008	0.000	0.006
findID	0.068	0.008	0.076
htmlPage	0.144	0.000	0.146
image	0.064	0.000	0.062
ma2D	0.000	0.000	0.002
maBoxplot	0.000	0.000	0.002
maColorBar	0.02	0.00	0.02
maCompCoord	0.004	0.000	0.005
maCompInd	0.004	0.000	0.006
maCompLayout	0.008	0.000	0.008
maCompNormA	0.004	0.000	0.002
maCompPlate	0.012	0.000	0.012
maCoord2Ind	0.004	0.000	0.005
maDefaultPar	0.000	0.000	0.003
maDotsDefaults	0.004	0.000	0.005
maDotsMatch	0.004	0.000	0.005
maGenControls	0.148	0.004	0.151
maGeneTable	0.112	0.000	0.113
maImage	0.836	0.012	0.883
maImage.func	0.000	0.000	0.002
maInd2Coord	0.008	0.000	0.006
maLegendLines	0.000	0.000	0.002
maLoess	0.000	0.000	0.002
maLoessLines	0.004	0.000	0.002
maMAD	0.004	0.000	0.001
maMed	0.004	0.000	0.002
maNorm	2.016	0.004	2.027
maNorm2D	0.000	0.000	0.002
maNormLoess	0.000	0.000	0.002
maNormMAD	0.000	0.000	0.001
maNormMain	12.877	0.004	12.903
maNormMed	0.004	0.000	0.002
maNormScale	0.388	0.000	0.385
maNum2Logic	0.000	0.004	0.002
maPalette	0.028	0.000	0.028
maPlot	2.276	0.004	2.283
maPlot.func	0.004	0.000	0.003
maSelectGnames	0.012	0.000	0.012
maText	0.004	0.000	0.003
maTop	0.004	0.000	0.005
mapGeneInfo	0.004	0.000	0.003
marrayInfo-class	0.004	0.000	0.002
marrayLayout-class	0.004	0.000	0.005
marrayNorm-class	0.384	0.004	0.390
marrayRaw-class	0.188	0.004	0.193
opVersionID	0.044	0.000	0.046
plotMA	1.952	0.008	1.964
read.Galfile	0.108	0.000	0.106
read.marrayInfo	0.044	0.000	0.045
read.marrayLayout	0.092	0.000	0.092
read.marrayRaw	2.128	0.012	2.146
rm.na	0.004	0.000	0.003
stat.confband.text	0.556	0.008	0.567
stat.gnames	0.296	0.000	0.296
write.list	0.140	0.000	0.138
write.marray	0.076	0.004	0.079
write.xls	0.100	0.000	0.103