BioC 3.3: CHECK report for baySeq on oaxaca

Package: baySeq

Version: 2.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings baySeq_2.6.0.tar.gz

StartedAt: 2016-10-12 23:29:02 -0700 (Wed, 12 Oct 2016)

EndedAt: 2016-10-12 23:33:10 -0700 (Wed, 12 Oct 2016)

EllapsedTime: 248.5 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_2.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/baySeq.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘2.6.0’
* 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 ... 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
.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’
.posteriorWeights: no visible binding for global variable ‘CDpriors’
.posteriorWeights: no visible binding for global variable ‘consensus’
bimodalSeparator : weighted.var: no visible global function definition
  for ‘weighted.mean’
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 : .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: 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 : 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’
getPriors.NB: no visible global function definition for ‘parApply’
getPriors.NB: no visible global function definition for ‘clusterEvalQ’
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:
  CDpriors DGEList abline axTicks axis calcNormFactors clustAssign
  clusterCall clusterEvalQ clusterExport consensus dbinom density
  dnbinom dnorm modifyList optim optimise optimize parApply parLapplyLB
  parRapply 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 70.843  0.312  71.297
getPriors      61.522  0.115  66.397
getLikelihoods 15.262  0.065  15.360
* 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
  ‘/Users/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	0.543	0.012	0.557
baySeq-classes	0.015	0.002	0.018
baySeq-package	70.843	0.312	71.297
bimodalSep	0.017	0.002	0.019
densityFunction	0.002	0.000	0.002
getLibsizes	0.008	0.001	0.009
getLikelihoods	15.262	0.065	15.360
getPosteriors	0.008	0.001	0.009
getPriors	61.522	0.115	66.397
getTPs	0.010	0.004	0.014
makeOrderings	0.053	0.003	0.055
plotMA.CD	0.014	0.001	0.015
plotPosteriors	0.012	0.002	0.014
plotPriors	0.017	0.002	0.019
selectTop	0.016	0.002	0.018
summarisePosteriors	0.008	0.001	0.010
topCounts	0.025	0.002	0.027