Package: yaqcaffy

Version: 1.18.0

Command: /home/biocbuild/bbs-2.11-bioc/R/bin/R CMD check --no-vignettes --timings yaqcaffy_1.18.0.tar.gz

StartedAt: 2013-03-25 05:40:27 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 05:44:27 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 240.3 seconds

RetCode: 0

Status:  OK

CheckDir: yaqcaffy.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/yaqcaffy.Rcheck’
* using R version 2.15.3 (2013-03-01)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘yaqcaffy/DESCRIPTION’ ... OK
* this is package ‘yaqcaffy’ version ‘1.18.0’
* 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 whether package ‘yaqcaffy’ can be installed ... OK
* checking installed package size ... OK
* 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 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 ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
getOutliers 40.951  0.352  41.485
getAllInt   18.769  0.288  19.174
getQCRatios  8.272  0.052   8.341
yaqc.affy    7.805  0.104   7.914
yaqc.plot    7.452  0.036   7.494
* 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
   ‘yaqcaffy.Rnw’ 
** testing if installed package can be loaded
No methods found in "Biobase" for requests: geneNames

* DONE (yaqcaffy)

name	user	system	elapsed
YaqcControlProbes-class	0.004	0.000	0.002
getAllInt	18.769	0.288	19.174
getBioProbes	0.432	0.008	0.439
getOutliers	40.951	0.352	41.485
getQCRatios	8.272	0.052	8.341
getRatioProbes	0.604	0.044	0.649
getSpikeProbes	0.724	0.012	0.735
probeSelectionInterface	0	0	0
reprodPlot	0.000	0.000	0.001
yaqc.affy	7.805	0.104	7.914
yaqc.plot	7.452	0.036	7.494