Package: edd

Version: 1.33.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch edd_1.33.0.tar.gz

StartedAt: 2012-02-29 00:24:44 -0800 (Wed, 29 Feb 2012)

EndedAt: 2012-02-29 00:26:16 -0800 (Wed, 29 Feb 2012)

EllapsedTime: 92.4 seconds

RetCode: 0

Status:  OK

CheckDir: edd.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.10-bioc/meat/edd.Rcheck'
* using R Under development (unstable) (2012-02-12 r58325)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'edd/DESCRIPTION' ... OK
* this is package 'edd' version '1.33.0'
* 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 'edd' 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
latEDtable: warning in matrix(x, nr = dd[1], nc = dd[2]): partial
  argument match of 'nr' to 'nrow'
latEDtable: warning in matrix(x, nr = dd[1], nc = dd[2]): partial
  argument match of 'nc' to 'ncol'
latEDtable: warning in matrix(x, nr = 1): partial argument match of
  'nr' to 'nrow'
makeCandmat.raw: warning in matrix(NA, nr = nRowPerCand * ncand, nc =
  nPerRow): partial argument match of 'nr' to 'nrow'
makeCandmat.raw: warning in matrix(NA, nr = nRowPerCand * ncand, nc =
  nPerRow): partial argument match of 'nc' to 'ncol'
mkt: warning in matrix(NA, nr = 140, nc = 50): partial argument match
  of 'nr' to 'nrow'
mkt: warning in matrix(NA, nr = 140, nc = 50): partial argument match
  of 'nc' to 'ncol'
* checking Rd files ... NOTE
prepare_Rd: maxKSp.Rd:20-21: 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/edd.Rcheck/00check.log'
for details.

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

* DONE (edd)

name	user	system	elapsed
centerScale	0.007	0.000	0.007
edd	15.544	0.109	15.655
eddDist-class	0.004	0.001	0.004
eddObsolete	22.956	0.072	23.031
flatQQNorm	0.004	0.000	0.004
latEDtable	3.754	0.015	3.769
makeCandmat.raw	0.002	0.001	0.002
maxKSp	0.038	0.000	0.038
plotED	0.035	0.009	0.044