BioC 3.2: CHECK report for compEpiTools on perceval

Package: compEpiTools

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings compEpiTools_1.4.0.tar.gz

StartedAt: 2015-10-27 06:45:58 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 06:54:36 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 518.0 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_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/compEpiTools.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.4.0’
* 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 ‘compEpiTools’ can be installed ... [38s/38s] 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
findLncRNA: no visible global function definition for ‘start<-’
findLncRNA: no visible global function definition for ‘end<-’
findLncRNA: no visible global function definition for ‘IRanges’
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’
TSS: no visible global function definition for ‘end<-’
TSS: no visible global function definition for ‘start<-’
ucsc2GRanges: no visible global function definition for ‘IRanges’
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’
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<-’
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<-’
makeGtfFromDb,TxDb: no visible global function definition for ‘reduce’
matchEnhancers,GRanges: no visible global function definition for
  ‘distanceToNearest’
matchEnhancers,GRanges: no visible global function definition for
  ‘IRanges’
* 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 ... [130s/156s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
topGOres                 54.184  1.710  56.207
makeGtfFromDb             7.372  0.417  13.047
GRannotate-methods        7.402  0.167   7.702
heatmapPlot               5.372  0.181   5.749
simplifyGOterms           1.938  0.200   5.337
getPromoterClass-methods  1.397  0.022  18.015
* 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-3.2-bioc/meat/compEpiTools.Rcheck/00check.log’
for details.

* installing *source* package ‘compEpiTools’ ...
** R
** inst
** preparing package for lazy loading
Warning: replacing previous import by ‘graph::.__C__dist’ when loading ‘topGO’

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import by ‘graph::.__C__dist’ when loading ‘topGO’

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

name	user	system	elapsed
GR2fasta-methods	0.864	0.010	0.908
GRanges2ucsc-methods	0.01	0.00	0.01
GRangesInPromoters-methods	4.051	0.100	4.151
GRannotate-methods	7.402	0.167	7.702
GRannotateSimple	1.437	0.034	1.471
GRbaseCoverage-methods	0.138	0.001	0.139
GRcoverage-methods	0.213	0.001	0.214
GRcoverageSummit-methods	0.102	0.000	0.103
GRenrichment-methods	0.117	0.001	0.118
GRmidpoint-methods	0.026	0.002	0.028
GRsetwidth	0.033	0.005	0.038
TSS	3.014	0.070	3.083
countOverlapsInBins-methods	0.160	0.000	0.161
distanceFromTSS-methods	3.808	0.056	3.864
enhancers	1.158	0.017	1.174
findLncRNA	1.673	0.030	1.825
getPromoterClass-methods	1.397	0.022	18.015
heatmapData	2.163	0.032	2.195
heatmapPlot	5.372	0.181	5.749
makeGtfFromDb	7.372	0.417	13.047
matchEnhancers	3.970	0.135	4.105
overlapOfGRanges-methods	0.082	0.000	0.082
palette2d	0.068	0.001	0.070
plotStallingIndex	3.718	0.088	3.916
simplifyGOterms	1.938	0.200	5.337
stallingIndex	3.913	0.090	4.003
topGOres	54.184	1.710	56.207
ucsc2GRanges	0.016	0.000	0.016
unionMaxScore-methods	0.127	0.000	0.127