BioC 2.12: CHECK report for marray on george2

Package: marray

Version: 1.38.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings marray_1.38.0.tar.gz

StartedAt: 2013-10-09 03:02:41 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 03:04:55 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 134.3 seconds

RetCode: 0

Status:  OK

CheckDir: marray.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/marray.Rcheck’
* using R version 3.0.1 (2013-05-16)
* 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 ‘1.38.0’
* 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/7s] OK
* checking installed package size ... NOTE
  installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc         1.7Mb
    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 ... [54s/54s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
maNormMain     21.974  0.024  22.076
read.marrayRaw  5.317  0.084   5.404
* 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
  ‘/home/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	1.568	0.016	1.590
checkTargetInfo	0.316	0.004	0.321
dim	0.028	0.000	0.029
findID	0.248	0.000	0.245
htmlPage	0.216	0.000	0.220
image	0.108	0.008	0.117
ma2D	0.024	0.000	0.023
maBoxplot	0.160	0.000	0.164
maColorBar	0.044	0.016	0.058
maCompCoord	0.012	0.000	0.013
maCompInd	0.020	0.000	0.018
maCompLayout	0.032	0.000	0.030
maCompNormA	0.016	0.000	0.016
maCompPlate	0.052	0.000	0.051
maCoord2Ind	0.012	0.004	0.018
maDefaultPar	0.000	0.008	0.009
maDotsDefaults	0.016	0.000	0.017
maDotsMatch	0.012	0.000	0.013
maGenControls	0.196	0.004	0.201
maGeneTable	0.108	0.012	0.118
maImage	2.100	0.016	2.128
maImage.func	0.012	0.000	0.012
maInd2Coord	0.02	0.00	0.02
maLegendLines	0.012	0.000	0.013
maLoess	0.016	0.000	0.013
maLoessLines	0.016	0.000	0.022
maMAD	0.016	0.000	0.013
maMed	0.012	0.000	0.011
maNorm	3.932	0.008	3.942
maNorm2D	0.004	0.004	0.010
maNormLoess	0.012	0.000	0.010
maNormMAD	0.16	0.00	0.16
maNormMain	21.974	0.024	22.076
maNormMed	0.016	0.004	0.021
maNormScale	1.148	0.020	1.170
maNum2Logic	0.012	0.000	0.012
maPalette	0.064	0.004	0.069
maPlot	4.076	0.032	4.467
maPlot.func	0.012	0.008	0.019
maSelectGnames	0.024	0.000	0.027
maText	0.012	0.000	0.012
maTop	0.012	0.000	0.010
mapGeneInfo	0.008	0.000	0.009
marrayInfo-class	0.144	0.000	0.142
marrayLayout-class	0.008	0.012	0.022
marrayNorm-class	0.844	0.020	0.867
marrayRaw-class	0.476	0.012	0.488
opVersionID	0.020	0.000	0.021
plotMA	3.392	0.004	3.401
read.Galfile	0.144	0.000	0.145
read.marrayInfo	0.104	0.000	0.105
read.marrayLayout	0.148	0.008	0.157
read.marrayRaw	5.317	0.084	5.404
rm.na	0.024	0.000	0.026
stat.confband.text	1.208	0.036	1.248
stat.gnames	0.588	0.008	0.593
write.list	0.328	0.000	0.329
write.marray	0.132	0.000	0.131
write.xls	0.204	0.004	0.208