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BioC 3.0: CHECK report for baySeq on oaxaca

This page was generated on 2015-04-10 10:03:47 -0700 (Fri, 10 Apr 2015).

Package 71/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
baySeq 2.0.50
Thomas J. Hardcastle
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/baySeq
Last Changed Rev: 95677 / Revision: 102249
Last Changed Date: 2014-10-17 04:38:16 -0700 (Fri, 17 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK 

Summary

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 21:34:57 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 21:41:36 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 399.5 seconds
RetCode: 0
Status:  OK 
CheckDir: baySeq.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /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-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 ‘2.0.50’
* 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 ... [12s/13s] 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/261s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
baySeq-package 123.339  0.262 126.017
getPriors      100.133  0.160 102.596
getLikelihoods  23.429  0.042  25.208
* 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.

baySeq.Rcheck/00install.out:

* 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)

baySeq.Rcheck/baySeq-Ex.timings:

nameusersystemelapsed
allModels0.9580.0110.975
baySeq-classes0.0230.0010.025
baySeq-package123.339 0.262126.017
bimodalSep0.0310.0010.032
densityFunction0.0020.0000.002
getLibsizes0.0120.0010.012
getLikelihoods23.429 0.04225.208
getPosteriors0.0120.0010.014
getPriors100.133 0.160102.596
getTPs0.0100.0030.013
makeOrderings0.0790.0010.080
plotMA.CD0.0180.0010.019
plotPosteriors0.0130.0010.015
plotPriors0.0150.0010.017
selectTop0.0290.0020.032
summarisePosteriors0.0080.0000.009
topCounts0.0500.0020.053