Multiple platform build/check report for BioC 3.14 - CHECK results for compEpiTools on tokay2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.4 LTS)	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4324
tokay2	Windows Server 2012 R2 Standard	x64	4.1.3 (2022-03-10) -- "One Push-Up"	4077
machv2	macOS 10.14.6 Mojave	x86_64	4.1.3 (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*

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### Running command:
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###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:compEpiTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings compEpiTools_1.28.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/compEpiTools.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... 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
** running examples for arch 'x64' ... 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: 2 ERRORs, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/compEpiTools.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/compEpiTools_1.28.0.tar.gz && rm -rf compEpiTools.buildbin-libdir && mkdir compEpiTools.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=compEpiTools.buildbin-libdir compEpiTools_1.28.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL compEpiTools_1.28.0.zip && rm compEpiTools_1.28.0.tar.gz compEpiTools_1.28.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
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  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 10 2064k   10  216k    0     0   811k      0  0:00:02 --:--:--  0:00:02  812k
100 2064k  100 2064k    0     0  1778k      0  0:00:01  0:00:01 --:--:-- 1780k

install for i386

* 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
  converting help for package 'compEpiTools'
    finding HTML links ... done
    GR2fasta-methods                        html  
    GRanges2ucsc-methods                    html  
    GRangesInPromoters-methods              html  
    GRannotate-methods                      html  
    GRannotateSimple                        html  
    GRbaseCoverage-methods                  html  
    GRcoverage-methods                      html  
    GRcoverageSummit-methods                html  
    GRenrichment-methods                    html  
    GRmidpoint-methods                      html  
    GRsetwidth                              html  
    TSS                                     html  
    compEpiTools-package                    html  
    countOverlapsInBins-methods             html  
    distanceFromTSS-methods                 html  
    enhancers                               html  
    findLncRNA                              html  
    getPromoterClass-methods                html  
    finding level-2 HTML links ... done

    heatmapData                             html  
    heatmapPlot                             html  
    makeGtfFromDb                           html  
    matchEnhancers                          html  
    overlapOfGRanges-methods                html  
    palette2d                               html  
    plotStallingIndex                       html  
    simplifyGOterms                         html  
    stallingIndex                           html  
    topGOres                                html  
    ucsc2GRanges                            html  
    unionMaxScore-methods                   html  
** 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

install for x64

* installing *source* package 'compEpiTools' ...
** testing if installed package can be loaded

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'
* MD5 sums
packaged installation of 'compEpiTools' as compEpiTools_1.28.0.zip
* DONE (compEpiTools)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'compEpiTools' successfully unpacked and MD5 sums checked

CHECK results for compEpiTools on tokay2

Summary

Command output

Installation output

Tests output

Example timings