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CHECK report for compEpiTools on malbec1

This page was generated on 2019-04-16 11:50:45 -0400 (Tue, 16 Apr 2019).

Package 312/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
compEpiTools 1.16.0
Kamal Kishore
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/compEpiTools
Branch: RELEASE_3_8
Last Commit: bfc46e8
Last Changed Date: 2018-10-30 11:41:54 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: compEpiTools
Version: 1.16.0
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:compEpiTools.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings compEpiTools_1.16.0.tar.gz
StartedAt: 2019-04-15 23:06:19 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 23:13:21 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 421.8 seconds
RetCode: 0
Status:  OK 
CheckDir: compEpiTools.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:compEpiTools.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings compEpiTools_1.16.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/compEpiTools.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (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 ‘1.16.0’
* 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 ... 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
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 : <anonymous>: no visible global function definition for
  'ggplot'
topGOres : <anonymous>: no visible global function definition for 'aes'
topGOres : <anonymous>: no visible binding for global variable
  'Significant'
topGOres : <anonymous>: no visible binding for global variable 'P_val'
topGOres : <anonymous>: no visible global function definition for
  'geom_bar'
topGOres : <anonymous>: no visible global function definition for
  'coord_flip'
topGOres : <anonymous>: 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'
Undefined global functions or variables:
  IRanges P_val Significant aes coord_flip distanceToNearest end<-
  geom_bar ggplot reduce seqlengths seqlengths<- start<- stopCluster
  trim txdb ylab
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
topGOres                 38.936  0.072  39.115
makeGtfFromDb             5.268  0.064   5.381
getPromoterClass-methods  1.040  0.060  16.810
* 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-3.8-bioc/meat/compEpiTools.Rcheck/00check.log’
for details.



Installation output

compEpiTools.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL compEpiTools
###
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘compEpiTools’ ...
** R
** inst
** byte-compile and prepare 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)

Tests output


Example timings

compEpiTools.Rcheck/compEpiTools-Ex.timings

nameusersystemelapsed
GR2fasta-methods0.4040.0000.425
GRanges2ucsc-methods0.0080.0000.006
GRangesInPromoters-methods3.5440.0563.603
GRannotate-methods3.8000.0163.820
GRannotateSimple0.5240.0080.530
GRbaseCoverage-methods0.0760.0040.081
GRcoverage-methods0.1000.0000.099
GRcoverageSummit-methods0.0400.0040.042
GRenrichment-methods0.0840.0000.084
GRmidpoint-methods0.0280.0000.027
GRsetwidth0.0360.0000.035
TSS1.7920.0121.804
countOverlapsInBins-methods0.1000.0000.098
distanceFromTSS-methods3.7640.0283.806
enhancers0.3200.0040.337
findLncRNA0.6680.0040.867
getPromoterClass-methods 1.04 0.0616.81
heatmapData1.0440.0481.093
heatmapPlot3.1600.0723.234
makeGtfFromDb5.2680.0645.381
matchEnhancers4.0720.1404.222
overlapOfGRanges-methods0.0840.0000.084
palette2d0.1120.0000.112
plotStallingIndex3.2840.0003.285
simplifyGOterms0.8920.0722.057
stallingIndex3.3480.0003.352
topGOres38.936 0.07239.115
ucsc2GRanges0.0120.0000.012
unionMaxScore-methods0.1320.0000.134