BioC 3.2: CHECK report for compEpiTools on oaxaca

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 02:36:29 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 02:44:22 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 473.3 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 (2015-08-14)
* 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 ‘1.4.0’
* 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 ... [36s/37s] 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’
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<-’
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’
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 ... [111s/136s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
topGOres                 45.491  1.866  47.692
makeGtfFromDb             6.609  0.360  15.198
GRannotate-methods        5.489  0.150   5.789
getPromoterClass-methods  1.055  0.022  15.903
* 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	0.735	0.012	0.997
GRanges2ucsc-methods	0.009	0.001	0.009
GRangesInPromoters-methods	3.485	0.080	3.569
GRannotate-methods	5.489	0.150	5.789
GRannotateSimple	1.069	0.025	1.098
GRbaseCoverage-methods	0.134	0.002	0.198
GRcoverage-methods	0.189	0.001	0.190
GRcoverageSummit-methods	0.106	0.000	0.107
GRenrichment-methods	0.113	0.005	0.118
GRmidpoint-methods	0.028	0.003	0.031
GRsetwidth	0.056	0.003	0.060
TSS	2.626	0.049	2.677
countOverlapsInBins-methods	0.186	0.000	0.187
distanceFromTSS-methods	3.923	0.063	3.995
enhancers	0.507	0.018	0.527
findLncRNA	0.928	0.028	0.983
getPromoterClass-methods	1.055	0.022	15.903
heatmapData	2.383	0.030	2.415
heatmapPlot	4.215	0.130	4.434
makeGtfFromDb	6.609	0.360	15.198
matchEnhancers	3.205	0.114	3.321
overlapOfGRanges-methods	0.071	0.000	0.072
palette2d	0.072	0.000	0.073
plotStallingIndex	3.548	0.071	3.624
simplifyGOterms	1.399	0.174	2.631
stallingIndex	3.495	0.110	3.606
topGOres	45.491	1.866	47.692
ucsc2GRanges	0.016	0.000	0.016
unionMaxScore-methods	0.157	0.000	0.157