BioC 3.0: CHECK report for baySeq on perceval

Package: baySeq

Version: 2.0.50

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch baySeq_2.0.50.tar.gz

StartedAt: 2015-04-09 22:57:30 -0700 (Thu, 09 Apr 2015)

EndedAt: 2015-04-09 23:04:40 -0700 (Thu, 09 Apr 2015)

EllapsedTime: 430.1 seconds

RetCode: 0

Status:  OK

CheckDir: baySeq.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch baySeq_2.0.50.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/baySeq.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘2.0.50’
* 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 ... [16s/18s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 dependencies in R code ... NOTE
'library' or 'require' call to ‘edgeR’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getLibsizes : estLibs: no visible global function definition for
  ‘DGEList’
getLibsizes : estLibs: no visible global function definition for
  ‘calcNormFactors’
getLikelihoods: no visible global function definition for ‘clusterCall’
getLikelihoods: no visible global function definition for ‘parLapply’
getLikelihoods: no visible global function definition for
  ‘clusterEvalQ’
getPosteriors: no visible global function definition for ‘clusterCall’
getPosteriors: no visible global function definition for ‘parRapply’
getPriors: no visible global function definition for ‘clusterCall’
getPriors: no visible global function definition for ‘parLapply’
getPriors: no visible global function definition for ‘clusterEvalQ’
getPriors.NB: no visible global function definition for ‘parApply’
getPriors.NB: no visible global function definition for ‘clusterEvalQ’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [254s/256s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
baySeq-package 124.745  0.241 125.207
getPriors       95.369  0.237  96.740
getLikelihoods  24.785  0.047  24.951
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/baySeq.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
allModels	1.067	0.016	1.083
baySeq-classes	0.025	0.003	0.028
baySeq-package	124.745	0.241	125.207
bimodalSep	0.035	0.003	0.037
densityFunction	0.003	0.001	0.003
getLibsizes	0.011	0.001	0.011
getLikelihoods	24.785	0.047	24.951
getPosteriors	0.010	0.002	0.012
getPriors	95.369	0.237	96.740
getTPs	0.011	0.005	0.016
makeOrderings	0.075	0.002	0.077
plotMA.CD	0.016	0.001	0.017
plotPosteriors	0.013	0.002	0.025
plotPriors	0.016	0.003	0.030
selectTop	0.034	0.003	0.038
summarisePosteriors	0.009	0.001	0.009
topCounts	0.048	0.004	0.052