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This page was generated on 2021-09-17 15:05:37 -0400 (Fri, 17 Sep 2021).

CHECK results for compEpiTools on nebbiolo1

To the developers/maintainers of the compEpiTools package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/compEpiTools.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 370/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
compEpiTools 1.26.0  (landing page)
Kamal Kishore
Snapshot Date: 2021-09-16 04:50:11 -0400 (Thu, 16 Sep 2021)
git_url: https://git.bioconductor.org/packages/compEpiTools
git_branch: RELEASE_3_13
git_last_commit: cefdb04
git_last_commit_date: 2021-05-19 12:06:54 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: compEpiTools
Version: 1.26.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:compEpiTools.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings compEpiTools_1.26.0.tar.gz
StartedAt: 2021-09-16 09:20:27 -0400 (Thu, 16 Sep 2021)
EndedAt: 2021-09-16 09:26:30 -0400 (Thu, 16 Sep 2021)
EllapsedTime: 362.8 seconds
RetCode: 0
Status:   OK  
CheckDir: compEpiTools.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:compEpiTools.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings compEpiTools_1.26.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/compEpiTools.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.26.0’
* 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 (user + system) or elapsed time > 5s
                           user system elapsed
topGOres                 25.048  0.424  25.473
getPromoterClass-methods  2.127  0.031  18.563
* 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-3.13-bioc/meat/compEpiTools.Rcheck/00check.log’
for details.



Installation output

compEpiTools.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL compEpiTools
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘compEpiTools’ ...
** using staged installation
** 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 from temporary location

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
** testing if installed package can be loaded from final location

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
** testing if installed package keeps a record of temporary installation path
* DONE (compEpiTools)

Tests output


Example timings

compEpiTools.Rcheck/compEpiTools-Ex.timings

nameusersystemelapsed
GR2fasta-methods1.6670.0281.696
GRanges2ucsc-methods0.0120.0000.012
GRangesInPromoters-methods2.0040.0752.081
GRannotate-methods3.5010.0683.570
GRannotateSimple0.6280.0240.651
GRbaseCoverage-methods0.1070.0000.107
GRcoverage-methods0.1380.0000.139
GRcoverageSummit-methods0.0860.0040.089
GRenrichment-methods0.0840.0000.084
GRmidpoint-methods0.0380.0040.042
GRsetwidth0.0570.0000.058
TSS1.3440.0401.383
countOverlapsInBins-methods0.1390.0000.140
distanceFromTSS-methods2.0570.0362.092
enhancers0.3780.0120.389
findLncRNA0.7050.0000.714
getPromoterClass-methods 2.127 0.03118.563
heatmapData1.0640.0321.096
heatmapPlot2.7200.1362.856
makeGtfFromDb4.3500.1684.616
matchEnhancers1.6630.0121.675
overlapOfGRanges-methods0.0610.0000.060
palette2d0.0430.0040.047
plotStallingIndex2.5480.0362.588
simplifyGOterms0.4950.0600.686
stallingIndex2.3760.1362.513
topGOres25.048 0.42425.473
ucsc2GRanges0.0210.0000.021
unionMaxScore-methods0.1350.0000.135