BioC 2.12: CHECK report for yaqcaffy on george2

Package: yaqcaffy

Version: 1.20.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings yaqcaffy_1.20.0.tar.gz

StartedAt: 2013-10-09 05:35:39 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 05:40:09 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 269.9 seconds

RetCode: 0

Status:  OK

CheckDir: yaqcaffy.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/yaqcaffy.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 ‘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 ... [21s/21s] 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 ... [107s/107s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
getOutliers 49.039  0.496  49.557
getAllInt   20.533  0.308  20.853
getQCRatios  9.401  0.132   9.533
yaqc.plot    8.476  0.044   8.523
yaqc.affy    8.357  0.036   8.391
* 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
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
* DONE (yaqcaffy)

name	user	system	elapsed
YaqcControlProbes-class	0.344	0.004	0.350
getAllInt	20.533	0.308	20.853
getBioProbes	0.576	0.016	0.592
getOutliers	49.039	0.496	49.557
getQCRatios	9.401	0.132	9.533
getRatioProbes	0.720	0.016	0.734
getSpikeProbes	0.736	0.016	0.750
probeSelectionInterface	0.000	0.000	0.003
reprodPlot	0.000	0.000	0.004
yaqc.affy	8.357	0.036	8.391
yaqc.plot	8.476	0.044	8.523