BioC 3.2: CHECK report for baySeq on linux1.bioconductor.org

Package: baySeq

Version: 2.4.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings baySeq_2.4.0.tar.gz

StartedAt: 2015-10-27 01:13:45 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 01:17:48 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 242.6 seconds

RetCode: 0

Status:  OK

CheckDir: baySeq.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings baySeq_2.4.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/baySeq.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘2.4.0’
* 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 ... [7s/7s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [163s/163s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
baySeq-package 79.793  0.059  79.905
getPriors      58.387  0.020  58.479
getLikelihoods 20.196  0.024  20.230
* 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-3.2-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	0.798	0.004	0.808
baySeq-classes	0.019	0.000	0.019
baySeq-package	79.793	0.059	79.905
bimodalSep	0.022	0.000	0.023
densityFunction	0.002	0.000	0.002
getLibsizes	0.013	0.000	0.012
getLikelihoods	20.196	0.024	20.230
getPosteriors	0.010	0.004	0.010
getPriors	58.387	0.020	58.479
getTPs	0.004	0.000	0.007
makeOrderings	0.032	0.000	0.032
plotMA.CD	0.012	0.000	0.012
plotPosteriors	0.009	0.000	0.008
plotPriors	0.01	0.00	0.01
selectTop	0.013	0.000	0.013
summarisePosteriors	0.005	0.000	0.005
topCounts	0.018	0.000	0.019