Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:07:49 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for compEpiTools on machv2


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? 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 379/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
compEpiTools 1.28.0  (landing page)
Kamal Kishore
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/compEpiTools
git_branch: RELEASE_3_14
git_last_commit: 7f99015
git_last_commit_date: 2021-10-26 12:15:25 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    ERROR  
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    ERROR    OK  
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: compEpiTools
Version: 1.28.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:compEpiTools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings compEpiTools_1.28.0.tar.gz
StartedAt: 2022-04-12 11:52:35 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 12:00:52 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 496.9 seconds
RetCode: 1
Status:   ERROR  
CheckDir: compEpiTools.Rcheck
Warnings: NA

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:compEpiTools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings compEpiTools_1.28.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/compEpiTools.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.28.0’
* 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
  'clusterApplyLB'
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 clusterApplyLB 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘compEpiTools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getPromoterClass
> ### Title: Determining the CpG promoter class and the average CpG content
> ### Aliases: getPromoterClass getPromoterClass-methods
> ###   getPromoterClass,TxDb-method
> ### Keywords: methods
> 
> ### ** Examples
> 
> require(BSgenome.Mmusculus.UCSC.mm9)
Loading required package: BSgenome.Mmusculus.UCSC.mm9
Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:graph':

    complement

The following object is masked from 'package:base':

    strsplit

Loading required package: rtracklayer
> require(TxDb.Mmusculus.UCSC.mm9.knownGene)
Loading required package: TxDb.Mmusculus.UCSC.mm9.knownGene
Loading required package: GenomicFeatures

Attaching package: 'GenomicFeatures'

The following object is masked from 'package:topGO':

    genes

> txdb <- TxDb.Mmusculus.UCSC.mm9.knownGene
> isActiveSeq(txdb) <- c(rep(FALSE,20), TRUE, rep(FALSE, 14))
> allpromoter <- getPromoterClass(txdb, Nproc=1, org=Mmusculus)
Error in clusterApplyLB(cl, chrs, pcChr, tssGR = tssGR, ORG = org) : 
  could not find function "clusterApplyLB"
Calls: getPromoterClass -> getPromoterClass
Execution halted
* 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 ERROR, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/compEpiTools.Rcheck/00check.log’
for details.


Installation output

compEpiTools.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL compEpiTools
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘compEpiTools’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
No methods found in package 'BiocGenerics' for requests: 'clusterApplyLB', 'clusterEvalQ' when loading 'methylPipe'
No methods found in package 'BiocGenerics' for requests: 'clusterApplyLB', 'clusterEvalQ' when loading 'compEpiTools'
** 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.
No methods found in package 'BiocGenerics' for requests: 'clusterApplyLB', 'clusterEvalQ' when loading 'methylPipe'
No methods found in package 'BiocGenerics' for requests: 'clusterApplyLB', 'clusterEvalQ' when loading 'compEpiTools'
** testing if installed package can be loaded from final location

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
No methods found in package 'BiocGenerics' for requests: 'clusterApplyLB', 'clusterEvalQ' when loading 'methylPipe'
No methods found in package 'BiocGenerics' for requests: 'clusterApplyLB', 'clusterEvalQ' when loading 'compEpiTools'
** testing if installed package keeps a record of temporary installation path
* DONE (compEpiTools)

Tests output


Example timings

compEpiTools.Rcheck/compEpiTools-Ex.timings

nameusersystemelapsed
GR2fasta-methods1.6850.0181.705
GRanges2ucsc-methods0.0240.0000.025
GRangesInPromoters-methods3.5560.0903.649
GRannotate-methods6.0320.0796.117
GRannotateSimple1.0440.0161.060
GRbaseCoverage-methods0.1290.0020.132
GRcoverage-methods0.1920.0030.195
GRcoverageSummit-methods0.1470.0020.149
GRenrichment-methods0.1460.0030.149
GRmidpoint-methods0.0780.0010.079
GRsetwidth0.1300.0040.135
TSS2.2270.0342.266
countOverlapsInBins-methods0.2480.0030.252
distanceFromTSS-methods3.5330.0283.563
enhancers0.6660.0100.677
findLncRNA1.2860.0251.315