BioC 3.3: CHECK report for baySeq on linux2.bioconductor.org

Package: baySeq

Version: 2.5.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings baySeq_2.5.0.tar.gz

StartedAt: 2015-10-27 01:54:00 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 01:58:01 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 241.4 seconds

RetCode: 0

Status:  OK

CheckDir: baySeq.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings baySeq_2.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/baySeq.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-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 ‘2.5.0’
* 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 ... [6s/6s] 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’
Undefined global functions or variables:
  CDpriors DGEList calcNormFactors clustAssign clusterCall clusterEvalQ
  clusterExport consensus parApply parLapplyLB parRapply
* 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 files in ‘vignettes’ ... OK
* checking examples ... [171s/171s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
baySeq-package 81.813  0.044  81.873
getPriors      67.556  0.032  67.854
getLikelihoods 17.920  0.004  17.939
* 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
  ‘/home/biocbuild/bbs-3.3-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	0.568	0.008	0.577
baySeq-classes	0.019	0.000	0.019
baySeq-package	81.813	0.044	81.873
bimodalSep	0.017	0.004	0.016
densityFunction	0.000	0.000	0.001
getLibsizes	0.004	0.000	0.006
getLikelihoods	17.920	0.004	17.939
getPosteriors	0.008	0.000	0.011
getPriors	67.556	0.032	67.854
getTPs	0.009	0.004	0.012
makeOrderings	0.049	0.008	0.056
plotMA.CD	0.024	0.000	0.023
plotPosteriors	0.011	0.004	0.014
plotPriors	0.016	0.000	0.016
selectTop	0.018	0.004	0.021
summarisePosteriors	0.008	0.000	0.009
topCounts	0.03	0.00	0.03