BioC 3.2: CHECK report for baySeq on oaxaca

Package: baySeq

Version: 2.4.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings baySeq_2.4.1.tar.gz

StartedAt: 2016-04-22 22:00:14 -0700 (Fri, 22 Apr 2016)

EndedAt: 2016-04-22 22:05:11 -0700 (Fri, 22 Apr 2016)

EllapsedTime: 297.0 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 baySeq_2.4.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/baySeq.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘2.4.1’
* 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 ... [9s/9s] 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.
Package in Depends field not imported from: ‘perm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.posteriorWeights: no visible binding for global variable ‘CDpriors’
.posteriorWeights: no visible binding for global variable ‘consensus’
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
  ‘clusterExport’
getLikelihoods: no visible global function definition for ‘clusterCall’
getLikelihoods: no visible global function definition for ‘parLapplyLB’
getLikelihoods: no visible global function definition for
  ‘clusterEvalQ’
getPosteriors: no visible global function definition for
  ‘clusterExport’
getPosteriors: no visible global function definition for ‘clusterCall’
getPosteriors: no visible binding for global variable ‘clustAssign’
getPosteriors: no visible global function definition for ‘parRapply’
getPriors: no visible global function definition for ‘clusterExport’
getPriors: no visible global function definition for ‘parLapplyLB’
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 ... [193s/202s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
baySeq-package 88.328  0.337  88.748
getPriors      81.523  0.159  89.740
getLikelihoods 17.071  0.174  17.257
* 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

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-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	0.659	0.016	0.675
baySeq-classes	0.018	0.002	0.019
baySeq-package	88.328	0.337	88.748
bimodalSep	0.023	0.003	0.026
densityFunction	0.001	0.000	0.002
getLibsizes	0.007	0.002	0.009
getLikelihoods	17.071	0.174	17.257
getPosteriors	0.013	0.003	0.015
getPriors	81.523	0.159	89.740
getTPs	0.011	0.003	0.014
makeOrderings	0.057	0.002	0.058
plotMA.CD	0.019	0.002	0.021
plotPosteriors	0.013	0.002	0.844
plotPriors	0.015	0.002	0.070
selectTop	0.021	0.003	0.023
summarisePosteriors	0.009	0.001	0.010
topCounts	0.032	0.003	0.034