Package: baySeq

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/2.11/Resources/bin/R CMD check --no-vignettes --timings baySeq_1.2.0.tar.gz

StartedAt: 2010-10-04 15:56:57 -0700 (Mon, 04 Oct 2010)

EndedAt: 2010-10-04 16:02:09 -0700 (Mon, 04 Oct 2010)

EllapsedTime: 312.1 seconds

RetCode: 0

Status:  OK

CheckDir: baySeq.Rcheck

Warnings: 0

* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.6-bioc/meat/baySeq.Rcheck'
* using R version 2.11.1 Patched (2010-05-31 r52167)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'baySeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'baySeq' version '1.2.0'
* 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 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
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 data for non-ASCII characters ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

* install options are ' --no-html'

* installing *source* package ‘baySeq’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (baySeq)

name	user	system	elapsed
baySeq-classes	0.052	0.006	0.058
baySeq-package	30.443	0.256	31.937
getLikelihoods	86.718	2.750	120.922
getPosteriors	0.663	0.007	0.803
getPriors	0.417	0.090	36.200
getTPs	30.512	0.319	31.619
plotPriors	33.751	0.073	34.127
topCounts	30.238	0.238	31.554