Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-30 11:34:58 -0400 (Thu, 30 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4753 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4518 |
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 418/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
compEpiTools 1.38.0 (landing page) Mattia Furlan
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
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: 1.38.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:compEpiTools.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings compEpiTools_1.38.0.tar.gz |
StartedAt: 2024-05-29 21:21:44 -0400 (Wed, 29 May 2024) |
EndedAt: 2024-05-29 21:29:47 -0400 (Wed, 29 May 2024) |
EllapsedTime: 482.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: compEpiTools.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:compEpiTools.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings compEpiTools_1.38.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/compEpiTools.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘compEpiTools/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘compEpiTools’ version ‘1.38.0’ * 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 loading without being on the library search path ... 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed topGOres 26.295 0.692 26.988 getPromoterClass-methods 0.751 0.028 21.416 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/home/biocbuild/bbs-3.19-bioc/meat/compEpiTools.Rcheck/00check.log’ for details.
compEpiTools.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL compEpiTools ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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 | 0.400 | 0.012 | 0.413 | |
GRanges2ucsc-methods | 0.008 | 0.000 | 0.008 | |
GRangesInPromoters-methods | 2.847 | 0.104 | 2.951 | |
GRannotate-methods | 3.451 | 0.084 | 3.536 | |
GRannotateSimple | 0.558 | 0.010 | 0.568 | |
GRbaseCoverage-methods | 0.061 | 0.000 | 0.060 | |
GRcoverage-methods | 0.111 | 0.000 | 0.110 | |
GRcoverageSummit-methods | 0.053 | 0.000 | 0.054 | |
GRenrichment-methods | 0.067 | 0.000 | 0.068 | |
GRmidpoint-methods | 0.023 | 0.000 | 0.023 | |
GRsetwidth | 0.032 | 0.000 | 0.033 | |
TSS | 1.200 | 0.032 | 1.232 | |
countOverlapsInBins-methods | 0.105 | 0.000 | 0.105 | |
distanceFromTSS-methods | 1.690 | 0.016 | 1.706 | |
enhancers | 1.409 | 0.016 | 1.425 | |
findLncRNA | 0.605 | 0.008 | 0.617 | |
getPromoterClass-methods | 0.751 | 0.028 | 21.416 | |
heatmapData | 0.957 | 0.144 | 1.101 | |
heatmapPlot | 2.596 | 0.246 | 2.842 | |
makeGtfFromDb | 2.745 | 0.254 | 3.000 | |
matchEnhancers | 1.693 | 0.040 | 1.733 | |
overlapOfGRanges-methods | 0.048 | 0.000 | 0.047 | |
palette2d | 0.043 | 0.004 | 0.046 | |
plotStallingIndex | 2.160 | 0.124 | 2.285 | |
simplifyGOterms | 0.417 | 0.084 | 0.572 | |
stallingIndex | 2.187 | 0.084 | 2.271 | |
topGOres | 26.295 | 0.692 | 26.988 | |
ucsc2GRanges | 0.013 | 0.000 | 0.013 | |
unionMaxScore-methods | 0.110 | 0.004 | 0.114 | |