Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-07-24 09:03 -0400 (Wed, 24 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4747 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4489 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4518 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4467 |
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 | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
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: 2024-07-21 23:02:03 -0400 (Sun, 21 Jul 2024) |
EndedAt: 2024-07-21 23:10:05 -0400 (Sun, 21 Jul 2024) |
EllapsedTime: 482.9 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 4.4.1 (2024-06-14) * 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 26.702 0.560 27.262 getPromoterClass-methods 0.860 0.013 20.294 * 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 | 0.519 | 0.004 | 0.525 | |
GRanges2ucsc-methods | 0.010 | 0.000 | 0.009 | |
GRangesInPromoters-methods | 3.346 | 0.112 | 3.459 | |
GRannotate-methods | 3.546 | 0.088 | 3.635 | |
GRannotateSimple | 0.661 | 0.045 | 0.707 | |
GRbaseCoverage-methods | 0.064 | 0.000 | 0.065 | |
GRcoverage-methods | 0.12 | 0.00 | 0.12 | |
GRcoverageSummit-methods | 0.053 | 0.000 | 0.054 | |
GRenrichment-methods | 0.07 | 0.00 | 0.07 | |
GRmidpoint-methods | 0.025 | 0.000 | 0.024 | |
GRsetwidth | 0.036 | 0.000 | 0.036 | |
TSS | 1.548 | 0.027 | 1.576 | |
countOverlapsInBins-methods | 0.112 | 0.000 | 0.112 | |
distanceFromTSS-methods | 1.720 | 0.013 | 1.732 | |
enhancers | 0.340 | 0.016 | 0.356 | |
findLncRNA | 1.998 | 0.159 | 2.162 | |
getPromoterClass-methods | 0.860 | 0.013 | 20.294 | |
heatmapData | 1.113 | 0.039 | 1.153 | |
heatmapPlot | 2.499 | 0.144 | 2.643 | |
makeGtfFromDb | 2.923 | 0.104 | 3.027 | |
matchEnhancers | 1.661 | 0.011 | 1.672 | |
overlapOfGRanges-methods | 0.046 | 0.000 | 0.046 | |
palette2d | 0.046 | 0.000 | 0.046 | |
plotStallingIndex | 2.307 | 0.012 | 2.321 | |
simplifyGOterms | 0.467 | 0.092 | 0.634 | |
stallingIndex | 2.260 | 0.048 | 2.308 | |
topGOres | 26.702 | 0.560 | 27.262 | |
ucsc2GRanges | 0.112 | 0.000 | 0.112 | |
unionMaxScore-methods | 0.120 | 0.000 | 0.121 | |