Back to Multiple platform build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-02-06 11:06:31 -0500 (Mon, 06 Feb 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" | 4483 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2023-01-10 r83596 ucrt) -- "Unsuffered Consequences" | 4249 |
merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" | 4272 |
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? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 389/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
compEpiTools 1.33.0 (landing page) Kamal Kishore
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
Package: compEpiTools |
Version: 1.33.0 |
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_1.33.0.tar.gz |
StartedAt: 2023-02-05 23:51:03 -0500 (Sun, 05 Feb 2023) |
EndedAt: 2023-02-06 00:08:26 -0500 (Mon, 06 Feb 2023) |
EllapsedTime: 1042.5 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: compEpiTools.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### 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_1.33.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/compEpiTools.Rcheck’ * using R Under development (unstable) (2023-01-10 r83596) * using platform: x86_64-apple-darwin17.0 (64-bit) * R was compiled by Apple clang version 12.0.0 (clang-1200.0.32.29) GNU Fortran (GCC) 8.2.0 * running under: macOS Mojave 10.14.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘compEpiTools/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘compEpiTools’ version ‘1.33.0’ * 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 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<-' 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 ... 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 ... WARNING Found the following significant warnings: Warning: 'applyPileups' is deprecated. Warning: 'applyPileups' is deprecated. Warning: 'applyPileups' is deprecated. Warning: 'applyPileups' is deprecated. Warning: 'applyPileups' is deprecated. Warning: 'applyPileups' is deprecated. Warning: 'applyPileups' is deprecated. Warning: 'applyPileups' is deprecated. Warning: 'applyPileups' is deprecated. Warning: 'applyPileups' is deprecated. Warning: 'applyPileups' is deprecated. Warning: 'applyPileups' is deprecated. Deprecated functions may be defunct as soon as of the next release of R. See ?Deprecated. Examples with CPU (user + system) or elapsed time > 5s user system elapsed topGOres 56.460 1.119 78.485 GRannotate-methods 6.908 0.095 9.495 makeGtfFromDb 5.887 0.350 8.444 heatmapPlot 5.589 0.276 7.642 distanceFromTSS-methods 5.275 0.044 7.238 GRangesInPromoters-methods 5.105 0.061 6.937 plotStallingIndex 4.722 0.043 6.348 stallingIndex 4.587 0.048 6.074 getPromoterClass-methods 1.299 0.062 49.618 * 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 WARNING, 1 NOTE See ‘/Users/biocbuild/bbs-3.17-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/4.3/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 | 0.853 | 0.053 | 1.265 | |
GRanges2ucsc-methods | 0.018 | 0.000 | 0.028 | |
GRangesInPromoters-methods | 5.105 | 0.061 | 6.937 | |
GRannotate-methods | 6.908 | 0.095 | 9.495 | |
GRannotateSimple | 1.189 | 0.026 | 1.607 | |
GRbaseCoverage-methods | 0.121 | 0.002 | 0.161 | |
GRcoverage-methods | 0.235 | 0.003 | 0.329 | |
GRcoverageSummit-methods | 0.119 | 0.002 | 0.156 | |
GRenrichment-methods | 0.140 | 0.003 | 0.199 | |
GRmidpoint-methods | 0.055 | 0.001 | 0.075 | |
GRsetwidth | 0.084 | 0.000 | 0.117 | |
TSS | 2.595 | 0.024 | 3.545 | |
countOverlapsInBins-methods | 0.256 | 0.001 | 0.350 | |
distanceFromTSS-methods | 5.275 | 0.044 | 7.238 | |
enhancers | 0.633 | 0.006 | 0.900 | |
findLncRNA | 1.285 | 0.023 | 1.814 | |
getPromoterClass-methods | 1.299 | 0.062 | 49.618 | |
heatmapData | 2.248 | 0.075 | 3.009 | |
heatmapPlot | 5.589 | 0.276 | 7.642 | |
makeGtfFromDb | 5.887 | 0.350 | 8.444 | |
matchEnhancers | 3.467 | 0.040 | 4.613 | |
overlapOfGRanges-methods | 0.113 | 0.000 | 0.157 | |
palette2d | 0.091 | 0.002 | 0.125 | |
plotStallingIndex | 4.722 | 0.043 | 6.348 | |
simplifyGOterms | 0.858 | 0.171 | 1.458 | |
stallingIndex | 4.587 | 0.048 | 6.074 | |
topGOres | 56.460 | 1.119 | 78.485 | |
ucsc2GRanges | 0.026 | 0.000 | 0.033 | |
unionMaxScore-methods | 0.249 | 0.002 | 0.366 | |