BioC 3.3: CHECK report for compEpiTools on morelia

Package: compEpiTools

Version: 1.5.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings compEpiTools_1.5.1.tar.gz

StartedAt: 2016-04-21 00:50:06 -0700 (Thu, 21 Apr 2016)

EndedAt: 2016-04-21 00:58:32 -0700 (Thu, 21 Apr 2016)

EllapsedTime: 506.5 seconds

RetCode: 0

Status:  OK

CheckDir: compEpiTools.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 compEpiTools_1.5.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/compEpiTools.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘compEpiTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘compEpiTools’ version ‘1.5.1’
* 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 ‘compEpiTools’ can be installed ... [38s/40s] 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
TSS: no visible global function definition for 'end<-'
TSS: no visible global function definition for 'start<-'
findLncRNA: no visible global function definition for 'start<-'
findLncRNA: no visible global function definition for 'end<-'
findLncRNA: no visible global function definition for 'IRanges'
findLncRNA: no visible binding for global variable 'quantile'
heatmapPlot: no visible global function definition for 'quantile'
heatmapPlot: no visible global function definition for 'hclust'
heatmapPlot: no visible global function definition for 'dist'
heatmapPlot: no visible global function definition for 'as.dendrogram'
plotStallingIndex: no visible global function definition for 'rainbow'
plotStallingIndex: no visible global function definition for 'layout'
plotStallingIndex: no visible global function definition for 'par'
plotStallingIndex: no visible global function definition for 'plot'
plotStallingIndex: no visible global function definition for 'points'
plotStallingIndex: no visible global function definition for 'legend'
stallingIndex : getBound: no visible global function definition for
  'start<-'
stallingIndex : getBound: no visible global function definition for
  'end<-'
stallingIndex: no visible global function definition for 'IRanges'
topGOres: no visible global function definition for 'ggplot'
topGOres: no visible global function definition for 'aes'
topGOres: no visible binding for global variable 'Significant'
topGOres: no visible binding for global variable 'P_val'
topGOres: no visible global function definition for 'geom_bar'
topGOres: no visible global function definition for 'coord_flip'
topGOres: no visible global function definition for 'ylab'
ucsc2GRanges: no visible global function definition for 'IRanges'
GR2fasta,GRanges: no visible global function definition for
  'seqlengths'
GR2fasta,GRanges: no visible global function definition for
  'seqlengths<-'
GR2fasta,GRanges: no visible global function definition for 'trim'
GRangesInPromoters,GRanges: no visible global function definition for
  'start<-'
GRannotate,GRanges: no visible global function definition for 'start<-'
GRannotate,GRanges: no visible global function definition for 'end<-'
GRannotateSimple,GRanges: no visible global function definition for
  'pie'
GRcoverageSummit,GRanges: no visible global function definition for
  'start<-'
GRcoverageSummit,GRanges: no visible global function definition for
  'end<-'
GRmidpoint,GRanges: no visible global function definition for 'start<-'
GRmidpoint,GRanges: no visible global function definition for 'end<-'
GRsetwidth,GRanges: no visible global function definition for 'start<-'
GRsetwidth,GRanges: no visible global function definition for 'end<-'
countOverlapsInBins,GRanges: no visible global function definition for
  'IRanges'
featuresLength,TxDb: no visible global function definition for 'reduce'
getPromoterClass,TxDb: no visible binding for global variable 'txdb'
getPromoterClass,TxDb: no visible global function definition for
  'start<-'
getPromoterClass,TxDb: no visible global function definition for
  'stopCluster'
makeGtfFromDb,TxDb: no visible global function definition for 'reduce'
makeGtfFromDb,TxDb: no visible global function definition for
  'write.table'
matchEnhancers,GRanges: no visible global function definition for
  'distanceToNearest'
matchEnhancers,GRanges: no visible global function definition for
  'IRanges'
Undefined global functions or variables:
  IRanges P_val Significant aes as.dendrogram coord_flip dist
  distanceToNearest end<- geom_bar ggplot hclust layout legend par pie
  plot points quantile rainbow reduce seqlengths seqlengths<- start<-
  stopCluster trim txdb write.table ylab
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "layout", "legend", "par", "pie", "plot",
             "points")
  importFrom("stats", "as.dendrogram", "dist", "hclust", "quantile")
  importFrom("utils", "write.table")
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [106s/149s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
topGOres                 42.084  1.574  44.119
GRannotate-methods        5.848  0.158   9.495
makeGtfFromDb             5.551  0.374  19.652
heatmapPlot               4.923  0.132   6.444
plotStallingIndex         3.925  0.077   5.925
getPromoterClass-methods  0.968  0.022  17.055
* 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-3.3-bioc/meat/compEpiTools.Rcheck/00check.log’
for details.

* installing *source* package ‘compEpiTools’ ...
** R
** inst
** preparing package for lazy loading

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
* DONE (compEpiTools)

name	user	system	elapsed
GR2fasta-methods	0.676	0.015	1.159
GRanges2ucsc-methods	0.009	0.000	0.009
GRangesInPromoters-methods	4.457	0.106	4.584
GRannotate-methods	5.848	0.158	9.495
GRannotateSimple	1.307	0.032	1.343
GRbaseCoverage-methods	0.128	0.002	0.377
GRcoverage-methods	0.176	0.002	0.177
GRcoverageSummit-methods	0.067	0.000	0.068
GRenrichment-methods	0.084	0.001	0.086
GRmidpoint-methods	0.02	0.00	0.02
GRsetwidth	0.027	0.001	0.028
TSS	2.132	0.071	2.206
countOverlapsInBins-methods	0.183	0.001	0.184
distanceFromTSS-methods	3.719	0.070	4.266
enhancers	0.510	0.021	0.554
findLncRNA	0.860	0.030	0.974
getPromoterClass-methods	0.968	0.022	17.055
heatmapData	1.761	0.036	3.374
heatmapPlot	4.923	0.132	6.444
makeGtfFromDb	5.551	0.374	19.652
matchEnhancers	3.139	0.127	3.277
overlapOfGRanges-methods	0.071	0.000	0.071
palette2d	0.119	0.004	0.126
plotStallingIndex	3.925	0.077	5.925
simplifyGOterms	1.429	0.194	3.554
stallingIndex	3.299	0.092	3.395
topGOres	42.084	1.574	44.119
ucsc2GRanges	0.016	0.000	0.016
unionMaxScore-methods	0.132	0.001	0.133