BioC 3.4: CHECK report for baySeq on morelia

Package: baySeq

Version: 2.8.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings baySeq_2.8.0.tar.gz

StartedAt: 2017-04-14 22:58:45 -0700 (Fri, 14 Apr 2017)

EndedAt: 2017-04-14 23:03:04 -0700 (Fri, 14 Apr 2017)

EllapsedTime: 259.2 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 baySeq_2.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/baySeq.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘2.8.0’
* 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 ... 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.betaBinomialFunction : dbetabinom: no visible global function
  definition for ‘dbinom’
.betaBinomialNCFunction : dbetabinom: no visible global function
  definition for ‘dbinom’
.bimodalKernel: no visible global function definition for ‘density’
.ciEstimator: no visible global function definition for ‘rbinom’
.ciEstimator: no visible global function definition for ‘quantile’
.dZINB: no visible global function definition for ‘dnbinom’
.nbinomDens: no visible global function definition for ‘dnbinom’
.normDensityFunction: no visible global function definition for ‘dnorm’
.oldmethObservables: no visible global function definition for ‘qbinom’
.oldmethObservables: no visible global function definition for ‘dbinom’
bimodalSeparator : weighted.var: no visible global function definition
  for ‘weighted.mean’
getPriors : .getSinglePriors: no visible global function definition for
  ‘optim’
getPriors : .getSinglePriors : groupValues: no visible global function
  definition for ‘optim’
getPriors : .getSinglePriors : groupValues: no visible global function
  definition for ‘optimise’
getPriors.NB : optimoverPriors : mualt: no visible global function
  definition for ‘dnbinom’
getPriors.NB : optimoverPriors : muZeros: no visible global function
  definition for ‘pnbinom’
getPriors.NB : optimoverPriors : dispML : <anonymous>: no visible
  global function definition for ‘dnbinom’
getPriors.NB : optimoverPriors : findDisp.QL: no visible global
  function definition for ‘optimise’
getPriors.NB : optimoverPriors : findDisp.QL : <anonymous>: no visible
  global function definition for ‘optimise’
getPriors.NB : optimoverPriors : findDisp.ML: no visible global
  function definition for ‘optim’
getPriors.NB : optimoverPriors : getMu: no visible global function
  definition for ‘optimize’
getPriors.NB : optimoverPriors : getMu: no visible global function
  definition for ‘optimise’
getPriors.NB: no visible global function definition for ‘quantile’
methObservables: no visible global function definition for ‘qbinom’
methObservables: no visible global function definition for ‘dbinom’
plotMA.CD: no visible global function definition for ‘plot’
plotMA.CD: no visible global function definition for ‘axis’
plotMA.CD: no visible global function definition for ‘axTicks’
plotMA.CD: no visible global function definition for ‘abline’
plotNullPrior: no visible global function definition for ‘density’
plotNullPrior: no visible global function definition for ‘modifyList’
plotNullPrior: no visible global function definition for ‘abline’
plotPosteriors: no visible global function definition for ‘plot’
plotPosteriors: no visible global function definition for ‘abline’
plotPosteriors: no visible global function definition for ‘axis’
plotPosteriors: no visible global function definition for ‘text’
plotPriors: no visible global function definition for ‘plot’
plotPriors: no visible global function definition for ‘density’
Undefined global functions or variables:
  abline axTicks axis dbinom density dnbinom dnorm modifyList optim
  optimise optimize plot pnbinom qbinom quantile rbinom text
  weighted.mean
Consider adding
  importFrom("graphics", "abline", "axTicks", "axis", "plot", "text")
  importFrom("stats", "dbinom", "density", "dnbinom", "dnorm", "optim",
             "optimise", "optimize", "pnbinom", "qbinom", "quantile",
             "rbinom", "weighted.mean")
  importFrom("utils", "modifyList")
to your NAMESPACE file.
* 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 ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
baySeq-package 75.476  0.242  75.925
getPriors      57.142  0.089  57.355
getLikelihoods 16.673  0.081  16.802
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.4-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	0.558	0.008	0.568
baySeq-classes	0.015	0.002	0.017
baySeq-package	75.476	0.242	75.925
bimodalSep	0.001	0.000	0.001
densityFunction	0.001	0.001	0.002
getLibsizes	0.009	0.001	0.011
getLikelihoods	16.673	0.081	16.802
getPosteriors	0.008	0.001	0.009
getPriors	57.142	0.089	57.355
getTPs	0.013	0.004	0.016
makeOrderings	0.051	0.002	0.052
marginaliseEqual	0.552	0.002	0.558
marginalisePairwise	0.540	0.002	0.543
plotMA.CD	0.015	0.002	0.017
plotPosteriors	0.014	0.002	0.016
plotPriors	0.014	0.001	0.016
selectTop	0.017	0.003	0.021
summarisePosteriors	0.007	0.002	0.008
topCounts	0.029	0.003	0.031