Package: baySeq

Version: 1.5.7

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch baySeq_1.5.7.tar.gz

StartedAt: 2011-03-17 15:37:10 -0700 (Thu, 17 Mar 2011)

EndedAt: 2011-03-17 15:47:18 -0700 (Thu, 17 Mar 2011)

EllapsedTime: 608.2 seconds

RetCode: 0

Status:  OK

CheckDir: baySeq.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/baySeq.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-03-06 r54683)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'baySeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'baySeq' version '1.5.7'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'baySeq' 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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
getPosteriors: no visible binding for global variable 'clustAssign'
getPosteriors: no visible binding for global variable 'getPostsEnv'
getPriors.NB: no visible global function definition for
  'estimateCommonDisp'
getPriors.NB: no visible global function definition for
  'estimateTagwiseDisp'
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package 'baySeq' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic for 'rbind' in package 'baySeq'
    (the supplied definition differs from and overrides the implicit generic
    in package 'base': Signatures differ:  (...), (deparse.level))
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (baySeq)

name	user	system	elapsed
baySeq-classes	0.035	0.002	0.037
baySeq-package	6.044	0.020	6.064
bimodalSep	0.001	0.000	0.001
getLikelihoods	138.669	0.734	170.117
getPosteriors	0.013	0.003	0.017
getPriors	0.822	0.074	36.484
getTPs	6.005	0.011	6.017
plotMA.CD	0.013	0.001	0.014
plotPosteriors	132.668	0.040	132.712
plotPriors	230.073	0.082	230.162
topCounts	5.866	0.006	5.872