BioC 2.13: CHECK report for yaqcaffy on zin1

Package: yaqcaffy

Version: 1.22.0

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings yaqcaffy_1.22.0.tar.gz

StartedAt: 2014-04-05 04:39:16 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 04:41:58 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 162.3 seconds

RetCode: 0

Status:  OK

CheckDir: yaqcaffy.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/yaqcaffy.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘1.22.0’
* 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
Packages in Depends field not imported from:
  ‘methods’ ‘simpleaffy’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ‘:::’ call: ‘simpleaffy:::.bg.stats’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘getAlpha1’ ‘getAlpha2’
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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘yaqcaffy.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [62s/62s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
getOutliers 27.086  0.256  27.420
getAllInt   10.384  0.180  10.612
getQCRatios  5.977  0.048   6.035
yaqc.affy    5.688  0.064   5.758
yaqc.plot    5.552  0.028   5.589
* 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 were 2 notes.
See
  ‘/home/biocbuild/bbs-2.13-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	0.136	0.004	0.142
getAllInt	10.384	0.180	10.612
getBioProbes	0.368	0.008	0.379
getOutliers	27.086	0.256	27.420
getQCRatios	5.977	0.048	6.035
getRatioProbes	0.516	0.016	0.535
getSpikeProbes	0.536	0.024	0.561
probeSelectionInterface	0	0	0
reprodPlot	0.028	0.000	0.027
yaqc.affy	5.688	0.064	5.758
yaqc.plot	5.552	0.028	5.589