BioC 3.4: CHECK report for epigenomix on malbec1

Package: epigenomix

Version: 1.14.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings epigenomix_1.14.0.tar.gz

StartedAt: 2017-04-14 22:20:26 -0400 (Fri, 14 Apr 2017)

EndedAt: 2017-04-14 22:24:00 -0400 (Fri, 14 Apr 2017)

EllapsedTime: 213.5 seconds

RetCode: 0

Status:  OK

CheckDir: epigenomix.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings epigenomix_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/epigenomix.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘epigenomix/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘epigenomix’ version ‘1.14.0’
* 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 ‘epigenomix’ 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 loading without being on the library search path ... 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
.bayesMixModel: no visible global function definition for ‘rgamma’
.bayesMixModel: no visible global function definition for ‘dnorm’
.bayesMixModel: no visible global function definition for ‘dexp’
.bayesMixModel: no visible global function definition for ‘dgamma’
.bayesMixModel: no visible binding for global variable ‘dnorm’
.bayesMixModel : <anonymous>: no visible global function definition for
  ‘dexp’
.bayesMixModel: no visible binding for global variable ‘dexp’
.bayesMixModel : <anonymous>: no visible global function definition for
  ‘dgamma’
.bayesMixModel: no visible binding for global variable ‘dgamma’
.mlMixModel: no visible binding for global variable ‘dnorm’
.mlMixModel : <anonymous>: no visible global function definition for
  ‘dexp’
.mlMixModel: no visible binding for global variable ‘dexp’
.mlMixModel: no visible global function definition for ‘dnorm’
.mlMixModel: no visible global function definition for ‘dexp’
.plotChains: no visible global function definition for ‘par’
.plotChains: no visible binding for global variable ‘plot’
.plotClassification: no visible binding for global variable ‘plot’
.plotClassification: no visible global function definition for ‘points’
.plotComponents: no visible binding for global variable ‘plot’
.plotComponents: no visible binding for global variable ‘hist’
.plotComponents: no visible global function definition for ‘lines’
.sampleAllocations: no visible global function definition for ‘dnorm’
.sampleAllocations: no visible global function definition for ‘dexp’
.sampleAllocations: no visible global function definition for ‘dgamma’
.sampleAllocations: no visible global function definition for ‘runif’
.sampleAlpha: no visible global function definition for ‘rnorm’
.sampleAlpha: no visible global function definition for ‘dnorm’
.sampleAlpha: no visible global function definition for ‘dgamma’
.sampleAlpha: no visible global function definition for ‘runif’
.sampleComponentParameters: no visible global function definition for
  ‘rgamma’
.sampleMixtureTDP: no visible global function definition for ‘rbeta’
.sampleShape: no visible global function definition for ‘dgamma’
.sampleShape: no visible global function definition for ‘rnorm’
.sampleShape: no visible global function definition for ‘dnorm’
.sampleShape: no visible global function definition for ‘runif’
bayesMixModel,numeric: no visible global function definition for
  ‘rgamma’
bayesMixModel,numeric: no visible global function definition for
  ‘dnorm’
bayesMixModel,numeric: no visible global function definition for ‘dexp’
bayesMixModel,numeric: no visible global function definition for
  ‘dgamma’
bayesMixModel,numeric: no visible binding for global variable ‘dnorm’
bayesMixModel,numeric : <anonymous>: no visible global function
  definition for ‘dexp’
bayesMixModel,numeric: no visible binding for global variable ‘dexp’
bayesMixModel,numeric : <anonymous>: no visible global function
  definition for ‘dgamma’
bayesMixModel,numeric: no visible binding for global variable ‘dgamma’
mlMixModel,numeric: no visible binding for global variable ‘dnorm’
mlMixModel,numeric : <anonymous>: no visible global function definition
  for ‘dexp’
mlMixModel,numeric: no visible binding for global variable ‘dexp’
mlMixModel,numeric: no visible global function definition for ‘dnorm’
mlMixModel,numeric: no visible global function definition for ‘dexp’
plotChains,MixModelBayes: no visible global function definition for
  ‘par’
plotChains,MixModelBayes: no visible binding for global variable ‘plot’
plotClassification,MixModel: no visible binding for global variable
  ‘plot’
plotClassification,MixModel: no visible global function definition for
  ‘points’
plotComponents,MixModel: no visible binding for global variable ‘plot’
plotComponents,MixModel: no visible binding for global variable ‘hist’
plotComponents,MixModel: no visible global function definition for
  ‘lines’
Undefined global functions or variables:
  dexp dgamma dnorm hist lines par plot points rbeta rgamma rnorm runif
Consider adding
  importFrom("graphics", "hist", "lines", "par", "plot", "points")
  importFrom("stats", "dexp", "dgamma", "dnorm", "rbeta", "rgamma",
             "rnorm", "runif")
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
plotChains    25.464  0.008  25.489
bayesMixModel 19.256  0.028  19.297
mlMixModel     8.484  0.012   8.497
* 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
  ‘/home/biocbuild/bbs-3.4-bioc/meat/epigenomix.Rcheck/00check.log’
for details.

* installing *source* package ‘epigenomix’ ...
** 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 (epigenomix)

name	user	system	elapsed
ChIPseqSet-class	0.000	0.000	0.001
MixModel-class	0	0	0
MixModelBayes-class	0.004	0.000	0.001
MixModelML-class	0	0	0
MixtureComponent-class	0	0	0
bayesMixModel	19.256	0.028	19.297
calculateCrossCorrelation	0.508	0.000	0.509
eSet	0.012	0.000	0.011
fpkm	0.032	0.000	0.031
getAlignmentQuality	0	0	0
integrateData	0.124	0.000	0.121
mappedReads	0.028	0.000	0.029
matchProbeToPromoter	0.196	0.000	0.195
mlMixModel	8.484	0.012	8.497
normalize	0.028	0.000	0.030
normalizeChIP	0.024	0.000	0.026
plotChains	25.464	0.008	25.489
plotClassification	0.044	0.000	0.044
plotComponents	0.052	0.004	0.054
summarizeReads	0.172	0.012	0.185
transToTSS	0.000	0.000	0.003