Package: baySeq

Version: 1.4.0

Command: /home/biocbuild/bbs-2.7-bioc/R/bin/R CMD check --no-vignettes --timings baySeq_1.4.0.tar.gz

StartedAt: 2011-04-07 04:53:01 -0700 (Thu, 07 Apr 2011)

EndedAt: 2011-04-07 04:56:41 -0700 (Thu, 07 Apr 2011)

EllapsedTime: 219.8 seconds

RetCode: 0

Status:  OK

CheckDir: baySeq.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.7-bioc/meat/baySeq.Rcheck’
* using R version 2.12.2 (2011-02-25)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘baySeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘baySeq’ version ‘1.4.0’
* 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
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 data for non-ASCII characters ... 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
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (baySeq)

name	user	system	elapsed
baySeq-classes	0.028	0.000	0.029
baySeq-package	18.745	0.004	18.753
getLikelihoods	55.543	0.028	70.232
getPosteriors	0.016	0.000	0.014
getPriors	0.296	0.040	21.410
getTPs	18.669	0.000	18.672
plotMA.CD	0.016	0.000	0.012
plotPosteriors	36.943	0.000	36.942
plotPriors	18.705	0.000	18.704
topCounts	18.525	0.008	18.532