BioC 2.14: CHECK report for yaqcaffy on zin2

Package: yaqcaffy

Version: 1.24.0

Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings yaqcaffy_1.24.0.tar.gz

StartedAt: 2014-10-08 03:49:11 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 03:51:42 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 151.2 seconds

RetCode: 0

Status:  OK

CheckDir: yaqcaffy.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings yaqcaffy_1.24.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/yaqcaffy.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘1.24.0’
* 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 ... [11s/11s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘simpleaffy:::.bg.stats’
  See the note in ?`:::` about the use of this operator.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 files in ‘vignettes’ ... OK
* checking examples ... [55s/55s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
getOutliers 24.662  0.216  24.956
getAllInt    8.868  0.124   9.036
getQCRatios  5.068  0.028   5.103
yaqc.affy    5.049  0.020   5.074
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  ‘/home/biocbuild/bbs-2.14-bioc/meat/yaqcaffy.Rcheck/00check.log’
for details.

* 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	0.004	0.000	0.002
getAllInt	8.868	0.124	9.036
getBioProbes	0.380	0.012	0.390
getOutliers	24.662	0.216	24.956
getQCRatios	5.068	0.028	5.103
getRatioProbes	0.488	0.012	0.502
getSpikeProbes	0.484	0.012	0.498
probeSelectionInterface	0	0	0
reprodPlot	0.000	0.000	0.001
yaqc.affy	5.049	0.020	5.074
yaqc.plot	4.748	0.020	4.777