Package: MCRestimate

Version: 2.12.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch MCRestimate_2.12.0.tar.gz

StartedAt: 2012-09-24 00:51:24 -0700 (Mon, 24 Sep 2012)

EndedAt: 2012-09-24 00:53:10 -0700 (Mon, 24 Sep 2012)

EllapsedTime: 106.0 seconds

RetCode: 0

Status:  OK

CheckDir: MCRestimate.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.10-bioc/meat/MCRestimate.Rcheck'
* using R version 2.15.1 (2012-06-22)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'MCRestimate/DESCRIPTION' ... OK
* this is package 'MCRestimate' version '2.12.0'
* 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 whether package 'MCRestimate' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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
MCRestimate.default : my.balanced.folds: warning in
  get("balanced.folds", en = asNamespace("pamr")): partial argument
  match of 'en' to 'envir'
important.variable.names : <anonymous>: warning in median(x, na =
  TRUE): partial argument match of 'na' to 'na.rm'
important.variable.names : <anonymous>: warning in var(x, na = TRUE):
  partial argument match of 'na' to 'na.rm'
plot.MCRestimate: warning in layout(c(1, 2), height = c(5, 1)): partial
  argument match of 'height' to 'heights'
* checking Rd files ... NOTE
prepare_Rd: PLR.Rd:19: Dropping empty section \details
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... OK
* 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

NOTE: There were 2 notes.
See
  '/Users/biocbuild/bbs-2.10-bioc/meat/MCRestimate.Rcheck/00check.log'
for details.

* installing *source* package 'MCRestimate' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'UsingMCRestimate.Rnw' 
** testing if installed package can be loaded

* DONE (MCRestimate)

name	user	system	elapsed
ClassifierBuild	8.319	0.152	8.481
MCRconfusion	2.258	0.124	2.394
MCRestimate	3.998	0.138	4.202
PLR	2.100	0.255	2.389
SVM.OVA.wrap	0	0	0
class.factor.format	0.115	0.008	0.123
geneReduction	0.003	0.000	0.004
important.variable.names	8.741	4.080	13.195
indVotes	2.207	0.049	2.257
intersectList	0.000	0.001	0.001
plot.MCRestimate	0.025	0.003	0.029
wrapper.fkt	8.999	3.273	12.338