BioC 2.12: CHECK report for stepNorm on petty

Package: stepNorm

Version: 1.32.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch stepNorm_1.32.0.tar.gz

StartedAt: 2013-10-09 00:02:06 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 00:05:54 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 227.8 seconds

RetCode: 0

Status:  OK

CheckDir: stepNorm.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/stepNorm.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'stepNorm/DESCRIPTION' ... OK
* this is package 'stepNorm' version '1.32.0'
* 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 'stepNorm' can be installed ... [5s/5s] 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 ... NOTE
loess2Dfit: warning in loess.control(trace.hat = "approximate",
  iteration = 5, surface = "direct"): partial argument match of
  'iteration' to 'iterations'
loessfit: warning in loess.control(trace.hat = "approximate", iteration
  = 5, surface = "direct"): partial argument match of 'iteration' to
  'iterations'
* 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 examples ... [163s/165s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
stepWithinNorm 68.426  0.448  69.469
fitWithin      60.464  0.222  61.602
fit2DWithin    27.224  0.225  27.748
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/stepNorm.Rcheck/00check.log'
for details.

* installing *source* package 'stepNorm' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (stepNorm)

name	user	system	elapsed
calcAIC	0.878	0.035	0.916
calcBIC	0.432	0.036	0.472
fit2DWithin	27.224	0.225	27.748
fitWithin	60.464	0.222	61.602
maCompPlate2	0.059	0.023	0.083
makeStepList	0.105	0.026	0.130
marrayFitClass	0.238	0.030	0.269
seqWithinNorm	1.078	0.117	1.201
stepWithinNorm	68.426	0.448	69.469
withinNorm	0.099	0.017	0.116