Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-05-30 12:36:42 -0400 (Thu, 30 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4669 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4404 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4431 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4384 |
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 |
Package 407/2233 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
compEpiTools 1.39.0 (landing page) Mattia Furlan
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
To the developers/maintainers of the compEpiTools package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: compEpiTools |
Version: 1.39.0 |
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_1.39.0.tar.gz |
StartedAt: 2024-05-29 22:57:20 -0400 (Wed, 29 May 2024) |
EndedAt: 2024-05-29 23:13:56 -0400 (Wed, 29 May 2024) |
EllapsedTime: 996.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: compEpiTools.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_1.39.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/compEpiTools.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘compEpiTools/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘compEpiTools’ version ‘1.39.0’ * 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 code 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<-' 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<- trim txdb ylab * checking Rd files ... NOTE checkRd: (-1) getPromoterClass-methods.Rd:21: Lost braces in \itemize; meant \describe ? checkRd: (-1) getPromoterClass-methods.Rd:22: Lost braces in \itemize; meant \describe ? checkRd: (-1) getPromoterClass-methods.Rd:23: Lost braces in \itemize; meant \describe ? checkRd: (-1) getPromoterClass-methods.Rd:24: Lost braces in \itemize; meant \describe ? checkRd: (-1) getPromoterClass-methods.Rd:25: Lost braces; missing escapes or markup? 25 | \item{downstream}:{numeric; number of bp downstream transcription start sites defining downstream limit of promoters} | ^ * 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 56.275 1.675 65.071 GRannotate-methods 8.023 0.216 9.108 makeGtfFromDb 6.235 0.578 8.467 heatmapPlot 6.280 0.393 7.664 GRangesInPromoters-methods 5.404 0.116 6.151 plotStallingIndex 5.307 0.092 6.108 stallingIndex 5.087 0.094 5.925 getPromoterClass-methods 1.522 0.053 44.839 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... 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-3.20-bioc/meat/compEpiTools.Rcheck/00check.log’ for details.
compEpiTools.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL compEpiTools ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/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 | 0.906 | 0.031 | 1.093 | |
GRanges2ucsc-methods | 0.021 | 0.001 | 0.025 | |
GRangesInPromoters-methods | 5.404 | 0.116 | 6.151 | |
GRannotate-methods | 8.023 | 0.216 | 9.108 | |
GRannotateSimple | 1.321 | 0.050 | 1.527 | |
GRbaseCoverage-methods | 0.138 | 0.004 | 0.147 | |
GRcoverage-methods | 0.270 | 0.005 | 0.296 | |
GRcoverageSummit-methods | 0.136 | 0.003 | 0.153 | |
GRenrichment-methods | 0.158 | 0.003 | 0.175 | |
GRmidpoint-methods | 0.066 | 0.001 | 0.073 | |
GRsetwidth | 0.094 | 0.002 | 0.102 | |
TSS | 2.736 | 0.039 | 3.044 | |
countOverlapsInBins-methods | 0.300 | 0.003 | 0.331 | |
distanceFromTSS-methods | 4.364 | 0.065 | 4.926 | |
enhancers | 0.694 | 0.014 | 0.753 | |
findLncRNA | 2.771 | 0.053 | 3.086 | |
getPromoterClass-methods | 1.522 | 0.053 | 44.839 | |
heatmapData | 2.484 | 0.084 | 2.827 | |
heatmapPlot | 6.280 | 0.393 | 7.664 | |
makeGtfFromDb | 6.235 | 0.578 | 8.467 | |
matchEnhancers | 3.851 | 0.088 | 4.542 | |
overlapOfGRanges-methods | 0.126 | 0.001 | 0.128 | |
palette2d | 0.107 | 0.010 | 0.134 | |
plotStallingIndex | 5.307 | 0.092 | 6.108 | |
simplifyGOterms | 0.921 | 0.268 | 1.732 | |
stallingIndex | 5.087 | 0.094 | 5.925 | |
topGOres | 56.275 | 1.675 | 65.071 | |
ucsc2GRanges | 0.029 | 0.001 | 0.034 | |
unionMaxScore-methods | 0.276 | 0.002 | 0.308 | |