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BioC 3.4: CHECK report for baySeq on morelia

This page was generated on 2017-04-15 16:23:04 -0400 (Sat, 15 Apr 2017).

Package 89/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
baySeq 2.8.0
Thomas J. Hardcastle
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/baySeq
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

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

Command output

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


* 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.


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
allModels0.5580.0080.568
baySeq-classes0.0150.0020.017
baySeq-package75.476 0.24275.925
bimodalSep0.0010.0000.001
densityFunction0.0010.0010.002
getLibsizes0.0090.0010.011
getLikelihoods16.673 0.08116.802
getPosteriors0.0080.0010.009
getPriors57.142 0.08957.355
getTPs0.0130.0040.016
makeOrderings0.0510.0020.052
marginaliseEqual0.5520.0020.558
marginalisePairwise0.5400.0020.543
plotMA.CD0.0150.0020.017
plotPosteriors0.0140.0020.016
plotPriors0.0140.0010.016
selectTop0.0170.0030.021
summarisePosteriors0.0070.0020.008
topCounts0.0290.0030.031