BioC 2.12: CHECK report for baySeq on george2

Package: baySeq

Version: 1.14.1

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings baySeq_1.14.1.tar.gz

StartedAt: 2013-10-09 00:18:33 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 00:25:53 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 440.0 seconds

RetCode: 0

Status:  OK

CheckDir: baySeq.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/baySeq.Rcheck’
* using R version 3.0.1 (2013-05-16)
* 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 ‘1.14.1’
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘baySeq’ can be installed ... [2s/2s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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
getLibsizes: no visible global function definition for ‘values’
getPosteriors: no visible binding for global variable ‘clustAssign’
getPosteriors: no visible binding for global variable ‘getPostsEnv’
getPriors.NB: no visible global function definition for
  ‘newSeqCountSet’
getPriors.NB: no visible global function definition for ‘estDispersion’
getTPs: no visible binding for global variable ‘logsum’
topCounts: no visible global function definition for ‘seqnames’
topCounts: no visible global function definition for ‘strand’
* 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 installed files from ‘inst/doc’ ... OK
* checking examples ... [393s/400s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
baySeq-package 198.624  0.140 201.780
getPriors      161.234  0.040 164.245
getLikelihoods  31.530  0.012  32.111
* 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 was 1 note.
See
  ‘/home/biocbuild/bbs-2.12-bioc/meat/baySeq.Rcheck/00check.log’
for details.

* 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
** installing vignettes
** testing if installed package can be loaded
* DONE (baySeq)

name	user	system	elapsed
baySeq-classes	0.172	0.004	0.176
baySeq-package	198.624	0.140	201.780
bimodalSep	0.004	0.008	0.011
getLibsizes	0.028	0.004	0.033
getLikelihoods	31.530	0.012	32.111
getPosteriors	0.136	0.004	0.139
getPriors	161.234	0.040	164.245
getTPs	0.036	0.008	0.042
plotMA.CD	0.184	0.004	0.189
plotPosteriors	0.020	0.008	0.028
plotPriors	0.036	0.004	0.039
topCounts	0.052	0.004	0.056