BioC 2.13: CHECK report for stepNorm on perceval

Package: stepNorm

Version: 1.34.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch stepNorm_1.34.0.tar.gz

StartedAt: 2014-04-05 04:39:55 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 04:42:31 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 155.6 seconds

RetCode: 0

Status:  OK

CheckDir: stepNorm.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/stepNorm.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘stepNorm/DESCRIPTION’ ... OK
* this is package ‘stepNorm’ version ‘1.34.0’
* 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 ... [4s/4s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘marray’ ‘methods’
A package should be listed in only one of these fields.
* 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 ... 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 ... [108s/109s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
stepWithinNorm 44.867  0.541  46.163
fitWithin      39.302  0.219  39.819
fit2DWithin    18.334  0.208  18.692
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-2.13-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	0.836	0.027	0.945
calcBIC	0.406	0.022	0.439
fit2DWithin	18.334	0.208	18.692
fitWithin	39.302	0.219	39.819
maCompPlate2	0.044	0.014	0.062
makeStepList	0.074	0.028	0.103
marrayFitClass	0.179	0.036	0.222
seqWithinNorm	0.762	0.084	0.866
stepWithinNorm	44.867	0.541	46.163
withinNorm	0.061	0.012	0.077