Package: pdmclass

Version: 1.30.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch pdmclass_1.30.0.tar.gz

StartedAt: 2013-03-25 00:46:49 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 00:48:18 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 88.9 seconds

RetCode: 0

Status:  OK

CheckDir: pdmclass.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/pdmclass.Rcheck'
* using R version 2.15.3 (2013-03-01)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'pdmclass/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'pdmclass' version '1.30.0'
* 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 'pdmclass' 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 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
pdmGenes: warning in match.call(expand = FALSE): partial argument match
  of 'expand' to 'expand.dots'
pdmGenes: warning in matrix(NA, nc = dim(x)[2], nr = dim(x)[1]):
  partial argument match of 'nr' to 'nrow'
pdmGenes: warning in matrix(NA, nc = dim(x)[2], nr = dim(x)[1]):
  partial argument match of 'nc' to 'ncol'
pdmGenes: warning in matrix(NA, nc = B, nr = list.length): partial
  argument match of 'nr' to 'nrow'
pdmGenes: warning in matrix(NA, nc = B, nr = list.length): partial
  argument match of 'nc' to 'ncol'
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
pdmClass.cv 26.913  7.136  35.570
pdmGenes    11.042  3.059  14.535
* 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 was 1 note.
See
  '/Users/biocbuild/bbs-2.11-bioc/meat/pdmclass.Rcheck/00check.log'
for details.

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

* DONE (pdmclass)

name	user	system	elapsed
pdmClass	1.509	0.234	1.862
pdmClass.cv	26.913	7.136	35.570
pdmGenes	11.042	3.059	14.535
predict.pls	0.696	0.185	0.975