| Back to Multiple platform build/check report for BioC 3.15 |
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This page was generated on 2022-03-18 11:07:14 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 | ||||
|
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. |
| Package 380/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| compEpiTools 1.29.4 (landing page) Kamal Kishore
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | ERROR | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | ERROR | OK | |||||||||
| Package: compEpiTools |
| Version: 1.29.4 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:compEpiTools.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings compEpiTools_1.29.4.tar.gz |
| StartedAt: 2022-03-17 18:47:34 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 18:53:06 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 331.7 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: compEpiTools.Rcheck |
| Warnings: NA |
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### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:compEpiTools.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings compEpiTools_1.29.4.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/compEpiTools.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* 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 '1.29.4'
* 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 ... WARNING
Found the following significant warnings:
Warning: Package 'compEpiTools' is deprecated and will be removed from
See 'D:/biocbuild/bbs-3.15-bioc/meat/compEpiTools.Rcheck/00install.out' for details.
* 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 ... 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 stopCluster(cl) : could not find function "stopCluster"
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 WARNING, 1 NOTE
See
'D:/biocbuild/bbs-3.15-bioc/meat/compEpiTools.Rcheck/00check.log'
for details.
compEpiTools.Rcheck/00install.out
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL compEpiTools
###
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* installing to library 'D:/biocbuild/bbs-3.15-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
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.
Warning: Package 'compEpiTools' is deprecated and will be removed from
Bioconductor version 3.16
** testing if installed package can be loaded from final location
groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.
Warning: Package 'compEpiTools' is deprecated and will be removed from
Bioconductor version 3.16
** testing if installed package keeps a record of temporary installation path
* DONE (compEpiTools)
Making 'packages.html' ... done
compEpiTools.Rcheck/compEpiTools-Ex.timings
| name | user | system | elapsed | |
| GR2fasta-methods | 0.67 | 0.04 | 0.72 | |
| GRanges2ucsc-methods | 0.01 | 0.00 | 0.01 | |
| GRangesInPromoters-methods | 2.66 | 0.11 | 2.76 | |
| GRannotate-methods | 3.84 | 0.09 | 3.94 | |
| GRannotateSimple | 0.56 | 0.13 | 0.69 | |
| GRbaseCoverage-methods | 0.14 | 0.00 | 0.14 | |
| GRcoverage-methods | 0.16 | 0.01 | 0.17 | |
| GRcoverageSummit-methods | 0.09 | 0.00 | 0.09 | |
| GRenrichment-methods | 0.11 | 0.00 | 0.11 | |
| GRmidpoint-methods | 0.02 | 0.00 | 0.02 | |
| GRsetwidth | 0.04 | 0.02 | 0.05 | |
| TSS | 1.43 | 0.03 | 1.47 | |
| countOverlapsInBins-methods | 0.14 | 0.00 | 0.14 | |
| distanceFromTSS-methods | 3.33 | 0.02 | 3.34 | |
| enhancers | 0.38 | 0.01 | 0.39 | |
| findLncRNA | 0.82 | 0.02 | 0.85 | |