| Back to Multiple platform build/check report for BioC 3.15 |
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This page was generated on 2022-10-19 13:22:45 -0400 (Wed, 19 Oct 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4386 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" | 4138 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4205 |
| 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 391/2140 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| compEpiTools 1.30.0 (landing page) Kamal Kishore
| nebbiolo1 | Linux (Ubuntu 20.04.5 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: 1.30.0 |
| 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_1.30.0.tar.gz |
| StartedAt: 2022-10-19 00:54:34 -0400 (Wed, 19 Oct 2022) |
| EndedAt: 2022-10-19 01:06:36 -0400 (Wed, 19 Oct 2022) |
| EllapsedTime: 721.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: compEpiTools.Rcheck |
| Warnings: 2 |
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### Running command:
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### /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_1.30.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/compEpiTools.Rcheck’
* using R version 4.2.1 (2022-06-23)
* 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 ‘1.30.0’
* 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 ... WARNING
Found the following significant warnings:
Warning: Package 'compEpiTools' is deprecated and will be removed from
See ‘/Users/biocbuild/bbs-3.15-bioc/meat/compEpiTools.Rcheck/00install.out’ for details.
* 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 54.385 1.373 55.837
GRannotate-methods 6.608 0.061 6.677
makeGtfFromDb 5.935 0.341 6.755
heatmapPlot 5.219 0.118 5.389
getPromoterClass-methods 1.239 0.027 33.280
* 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 WARNINGs, 1 NOTE
See
‘/Users/biocbuild/bbs-3.15-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/4.2/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. Warning: Package 'compEpiTools' is deprecated and will be removed from Bioconductor version 3.16 ** testing if installed package can be loaded from final location groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built. Warning: Package 'compEpiTools' is deprecated and will be removed from Bioconductor version 3.16 ** testing if installed package keeps a record of temporary installation path * DONE (compEpiTools)
compEpiTools.Rcheck/compEpiTools-Ex.timings
| name | user | system | elapsed | |
| GR2fasta-methods | 1.918 | 0.019 | 1.942 | |
| GRanges2ucsc-methods | 0.015 | 0.000 | 0.016 | |
| GRangesInPromoters-methods | 3.628 | 0.082 | 3.715 | |
| GRannotate-methods | 6.608 | 0.061 | 6.677 | |
| GRannotateSimple | 2.291 | 0.016 | 2.308 | |
| GRbaseCoverage-methods | 0.179 | 0.001 | 0.182 | |
| GRcoverage-methods | 0.221 | 0.002 | 0.223 | |
| GRcoverageSummit-methods | 0.118 | 0.002 | 0.120 | |
| GRenrichment-methods | 0.136 | 0.002 | 0.138 | |
| GRmidpoint-methods | 0.040 | 0.000 | 0.041 | |
| GRsetwidth | 0.077 | 0.001 | 0.078 | |
| TSS | 2.270 | 0.061 | 2.334 | |
| countOverlapsInBins-methods | 0.276 | 0.029 | 0.305 | |
| distanceFromTSS-methods | 3.724 | 0.049 | 3.783 | |
| enhancers | 0.625 | 0.008 | 0.635 | |
| findLncRNA | 1.286 | 0.026 | 1.319 | |
| getPromoterClass-methods | 1.239 | 0.027 | 33.280 | |
| heatmapData | 2.164 | 0.020 | 2.186 | |
| heatmapPlot | 5.219 | 0.118 | 5.389 | |
| makeGtfFromDb | 5.935 | 0.341 | 6.755 | |
| matchEnhancers | 3.359 | 0.036 | 3.401 | |
| overlapOfGRanges-methods | 0.108 | 0.000 | 0.109 | |
| palette2d | 0.089 | 0.004 | 0.094 | |
| plotStallingIndex | 4.549 | 0.037 | 4.599 | |
| simplifyGOterms | 0.804 | 0.161 | 1.076 | |
| stallingIndex | 4.489 | 0.044 | 4.542 | |
| topGOres | 54.385 | 1.373 | 55.837 | |
| ucsc2GRanges | 0.024 | 0.001 | 0.024 | |
| unionMaxScore-methods | 0.238 | 0.015 | 0.252 | |