Package: arrayQuality

Version: 1.30.0

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch arrayQuality_1.30.0.tar.gz

StartedAt: 2011-10-20 13:28:27 -0700 (Thu, 20 Oct 2011)

EndedAt: 2011-10-20 13:29:30 -0700 (Thu, 20 Oct 2011)

EllapsedTime: 62.5 seconds

RetCode: 0

Status:  OK

CheckDir: arrayQuality.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/arrayQuality.Rcheck'
* using R version 2.13.2 (2011-09-30)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'arrayQuality/DESCRIPTION' ... OK
* this is package 'arrayQuality' version '1.30.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'arrayQuality' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 45.8Mb
  sub-directories of 1Mb or more:
    doc         1.3Mb
    gprQCData  14.9Mb
    Heebo      17.1Mb
    Meebo      12.2Mb
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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
PRvQCHyb: no visible binding for global variable 'MmDEGenes'
Spike.Cy5vsCy3: no visible binding for global variable 'MEEBOset'
Spike.Cy5vsCy3: no visible binding for global variable 'RG'
Spike.Individual.Sensitivity: no visible binding for global variable
  'RG'
Spike.Individual.Sensitivity: no visible binding for global variable
  'MEEBOset'
Spike.Individual.Sensitivity: no visible binding for global variable
  'MEEBOctrl'
Spike.MM.Scatter: no visible binding for global variable 'RG'
Spike.MM.Scatter: no visible binding for global variable 'MEEBOset'
Spike.MMplot: no visible binding for global variable 'RG'
Spike.MMplot: no visible binding for global variable 'MEEBOset'
Spike.Sensitivity: no visible binding for global variable 'RG'
Spike.Sensitivity: no visible binding for global variable 'MEEBOset'
arrayScal: no visible binding for global variable 'MmReferenceDB'
getSpikeIds: no visible binding for global variable 'MEEBOset'
getSpikeIndex: no visible binding for global variable 'MEEBOset'
heeboQuality: no visible binding for global variable 'HEEBOset'
heeboQuality: no visible binding for global variable 'HEEBOctrl'
heeboQuality: no visible binding for global variable 'HEEBOtilingres'
heeboQualityPlots: no visible binding for global variable 'HEEBOset'
meeboQuality: no visible binding for global variable 'MEEBOset'
meeboQuality: no visible binding for global variable 'MEEBOctrl'
meeboQuality: no visible binding for global variable 'MEEBOtilingres'
meeboQualityPlots: no visible binding for global variable 'MEEBOset'
qpBEplot.linear: no visible binding for global variable 'MEEBOctrl'
qpBoxplotMeebo: no visible binding for global variable 'MEEBOset'
qpDotPlotsEEBO: no visible binding for global variable 'MEEBOset'
qpDotPlotsMeebo: no visible binding for global variable 'MEEBOset'
qpMisMatchPlot: no visible binding for global variable 'HEEBOctrl'
qpTiling: no visible binding for global variable 'MEEBOtilingres'
qualBoxplot: no visible binding for global variable 'MmReferenceDB'
qualBoxplot: no visible binding for global variable 'HsReferenceDB'
qualityScore: no visible binding for global variable 'MmReferenceDB'
readAllSpikes: no visible binding for global variable 'MEEBOset'
scaleRefTable: no visible binding for global variable 'MmReferenceDB'
* checking Rd files ... NOTE
prepare_Rd: spotQuality.Rd:92-93: Dropping empty section \examples
* 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 examples ... OK
* checking PDF version of manual ... OK

* installing *source* package 'arrayQuality' ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: limma
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (arrayQuality)

name	user	system	elapsed
PRv9mers	0.002	0.001	0.005
PRvQCHyb	0.003	0.002	0.004
agQuality	0.001	0.000	0.002
globalQuality	0.003	0.001	0.004
gpQuality	0.003	0.001	0.004
heeboQuality	0	0	0
heeboQualityPlots	0.001	0.000	0.001
maQualityPlots	0.001	0.000	0.001
meeboQuality	0.000	0.000	0.001
meeboQualityPlots	0.001	0.000	0.001
qualBoxplot	0.003	0.002	0.005
readGPR	0.003	0.001	0.004
readSpikeTypes	0.003	0.001	0.003
slideQuality	0.003	0.001	0.003