Package: pdmclass

Version: 1.28.0

Command: /home/biocbuild/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings pdmclass_1.28.0.tar.gz

StartedAt: 2012-09-24 02:48:38 -0700 (Mon, 24 Sep 2012)

EndedAt: 2012-09-24 02:50:01 -0700 (Mon, 24 Sep 2012)

EllapsedTime: 82.8 seconds

RetCode: 0

Status:  OK

CheckDir: pdmclass.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/pdmclass.Rcheck’
* using R version 2.15.1 (2012-06-22)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pdmclass/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pdmclass’ version ‘1.28.0’
* 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 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 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 was 1 note.
See
  ‘/loc/home/biocbuild/bbs-2.10-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	2.008	0.052	2.099
pdmClass.cv	35.110	0.612	35.773
pdmGenes	14.533	0.244	14.823
predict.pls	0.680	0.004	0.683