Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:32 -0400 (Fri, 15 Oct 2021).
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 370/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
compEpiTools 1.26.0 (landing page) Kamal Kishore
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: compEpiTools |
Version: 1.26.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:compEpiTools.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings compEpiTools_1.26.0.tar.gz |
StartedAt: 2021-10-14 17:42:27 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 17:51:05 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 518.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: compEpiTools.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:compEpiTools.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings compEpiTools_1.26.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/compEpiTools.Rcheck’ * using R version 4.1.1 (2021-08-10) * 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 ‘1.26.0’ * 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 ... NOTE Found the following hidden files and directories: .git_fetch_output.txt .git_merge_output.txt These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed topGOres 39.918 2.636 42.580 GRannotate-methods 5.380 0.072 5.458 makeGtfFromDb 4.588 0.315 5.310 getPromoterClass-methods 1.260 0.031 29.194 * 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 NOTEs See ‘/Users/biocbuild/bbs-3.13-bioc/meat/compEpiTools.Rcheck/00check.log’ for details.
compEpiTools.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/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. ** 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)
compEpiTools.Rcheck/compEpiTools-Ex.timings
name | user | system | elapsed | |
GR2fasta-methods | 1.635 | 0.021 | 1.659 | |
GRanges2ucsc-methods | 0.016 | 0.001 | 0.016 | |
GRangesInPromoters-methods | 2.973 | 0.077 | 3.052 | |
GRannotate-methods | 5.380 | 0.072 | 5.458 | |
GRannotateSimple | 0.767 | 0.013 | 0.781 | |
GRbaseCoverage-methods | 0.145 | 0.002 | 0.147 | |
GRcoverage-methods | 0.185 | 0.002 | 0.188 | |
GRcoverageSummit-methods | 0.113 | 0.002 | 0.114 | |
GRenrichment-methods | 0.148 | 0.003 | 0.150 | |
GRmidpoint-methods | 0.072 | 0.001 | 0.073 | |
GRsetwidth | 0.124 | 0.001 | 0.126 | |
TSS | 2.347 | 0.065 | 2.413 | |
countOverlapsInBins-methods | 0.284 | 0.001 | 0.284 | |
distanceFromTSS-methods | 3.486 | 0.030 | 3.518 | |
enhancers | 0.690 | 0.011 | 0.701 | |
findLncRNA | 1.136 | 0.018 | 1.159 | |
getPromoterClass-methods | 1.260 | 0.031 | 29.194 | |
heatmapData | 2.688 | 0.018 | 2.708 | |
heatmapPlot | 4.406 | 0.211 | 4.667 | |
makeGtfFromDb | 4.588 | 0.315 | 5.310 | |
matchEnhancers | 2.938 | 0.049 | 2.987 | |
overlapOfGRanges-methods | 0.183 | 0.008 | 0.191 | |
palette2d | 0.076 | 0.004 | 0.079 | |
plotStallingIndex | 4.052 | 0.035 | 4.092 | |
simplifyGOterms | 0.618 | 0.131 | 0.829 | |
stallingIndex | 3.754 | 0.026 | 3.782 | |
topGOres | 39.918 | 2.636 | 42.580 | |
ucsc2GRanges | 0.033 | 0.001 | 0.034 | |
unionMaxScore-methods | 0.282 | 0.002 | 0.284 | |