BioC 2.14: CHECK report for baySeq on petty

Package: baySeq

Version: 1.18.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch baySeq_1.18.0.tar.gz

StartedAt: 2014-10-07 20:50:34 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 20:59:04 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 510.2 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_1.18.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/baySeq.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘1.18.0’
* 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 ... [15s/16s] 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
Packages in Depends field not imported from:
  ‘GenomicRanges’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of 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
getLikelihoods : distFunctionConsensus: no visible binding for global
  variable ‘seglen’
getLikelihoods : LNbootStrap : PDgivenr.LNConsensus: no visible binding
  for global variable ‘prior’
getPosteriors: no visible binding for global variable ‘clustAssign’
getPosteriors: no visible binding for global variable ‘getPostsEnv’
getPriors.NB: no visible global function definition for
  ‘newSeqCountSet’
getPriors.NB: no visible global function definition for ‘estDispersion’
getTPs: no visible binding for global variable ‘logsum’
* 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 ... [336s/343s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
baySeq-package 163.065  0.337 165.563
getPriors      145.664  0.305 149.948
getLikelihoods  19.526  0.032  19.691
* 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

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/baySeq.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
baySeq-classes	0.084	0.006	0.091
baySeq-package	163.065	0.337	165.563
bimodalSep	0.002	0.000	0.002
getLibsizes	0.020	0.001	0.020
getLikelihoods	19.526	0.032	19.691
getPosteriors	0.020	0.003	0.022
getPriors	145.664	0.305	149.948
getTPs	0.009	0.005	0.014
plotMA.CD	0.026	0.001	0.028
plotPosteriors	0.015	0.002	0.018
plotPriors	0.018	0.002	0.022
topCounts	0.028	0.002	0.030