Package: yaqcaffy

Version: 1.20.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch yaqcaffy_1.20.0.tar.gz

StartedAt: 2013-05-01 11:57:01 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 12:02:12 -0700 (Wed, 01 May 2013)

EllapsedTime: 310.8 seconds

RetCode: 0

Status:  OK

CheckDir: yaqcaffy.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/yaqcaffy.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'yaqcaffy/DESCRIPTION' ... OK
* this is package 'yaqcaffy' version '1.20.0'
* 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 'yaqcaffy' can be installed ... [17s/18s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* 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 ... OK
* 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 installed files from 'inst/doc' ... OK
* checking examples ... [142s/143s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
getOutliers 59.581  2.464  62.149
getAllInt   24.117  0.972  25.252
getQCRatios 14.298  0.966  15.350
yaqc.affy   13.161  0.998  14.159
yaqc.plot   12.387  0.809  13.196
* 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

* installing *source* package 'yaqcaffy' ...
** R
** inst
** preparing package for lazy loading
No methods found in "Biobase" for requests: geneNames
Creating a generic function for 'summary' from package 'base' in package 'yaqcaffy'
Creating a generic function for 'merge' from package 'base' in package 'yaqcaffy'
Creating a generic function for 'identical' from package 'base' in package 'yaqcaffy'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "Biobase" for requests: geneNames
* DONE (yaqcaffy)

name	user	system	elapsed
YaqcControlProbes-class	0.017	0.008	0.024
getAllInt	24.117	0.972	25.252
getBioProbes	0.887	0.042	0.936
getOutliers	59.581	2.464	62.149
getQCRatios	14.298	0.966	15.350
getRatioProbes	1.297	0.089	1.386
getSpikeProbes	1.251	0.040	1.303
probeSelectionInterface	0.003	0.005	0.008
reprodPlot	0.003	0.006	0.009
yaqc.affy	13.161	0.998	14.159
yaqc.plot	12.387	0.809	13.196