Package: baySeq

Version: 1.7.1

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch baySeq_1.7.1.tar.gz

StartedAt: 2011-07-07 01:38:44 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 01:54:10 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 925.9 seconds

RetCode: 0

Status:  OK

CheckDir: baySeq.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/baySeq.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-22 r56208)
* 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 '1.7.1'
* 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 sizes of PDF files under '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

* installing *source* package 'baySeq' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for "rbind" in package "baySeq"
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'baySeq.Rnw' 
** testing if installed package can be loaded

* DONE (baySeq)

name	user	system	elapsed
baySeq-classes	0.055	0.007	0.067
baySeq-package	8.395	0.104	8.928
bimodalSep	0.001	0.000	0.001
getLikelihoods	190.569	2.667	271.228
getPosteriors	0.050	0.014	0.065
getPriors	0.501	0.095	70.252
getTPs	8.265	0.105	8.521
plotMA.CD	0.018	0.003	0.021
plotPosteriors	183.171	2.715	197.925
plotPriors	319.695	1.070	328.385
topCounts	8.255	0.100	8.519