| Back to Mac ARM64 build report for BioC 3.17 |
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This page was generated on 2023-10-20 09:38:00 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| 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 409/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| compEpiTools 1.34.1 (landing page) Mattia Furlan
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | WARNINGS | OK |  | |||||||
|
To the developers/maintainers of the compEpiTools package: - 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: 1.34.1 |
| 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_1.34.1.tar.gz |
| StartedAt: 2023-10-17 11:19:05 -0400 (Tue, 17 Oct 2023) |
| EndedAt: 2023-10-17 11:31:13 -0400 (Tue, 17 Oct 2023) |
| EllapsedTime: 727.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: compEpiTools.Rcheck |
| Warnings: 1 |
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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_1.34.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/compEpiTools.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* 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 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘compEpiTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘compEpiTools’ version ‘1.34.1’
* 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 40.566 1.009 62.815
makeGtfFromDb 4.762 0.159 7.608
GRannotate-methods 4.348 0.114 7.280
GRangesInPromoters-methods 3.524 0.081 6.083
heatmapPlot 3.404 0.166 5.375
getPromoterClass-methods 1.962 0.045 33.987
* 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-mac-arm64/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-arm64/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 | 0.646 | 0.033 | 1.036 | |
| GRanges2ucsc-methods | 0.010 | 0.000 | 0.015 | |
| GRangesInPromoters-methods | 3.524 | 0.081 | 6.083 | |
| GRannotate-methods | 4.348 | 0.114 | 7.280 | |
| GRannotateSimple | 0.810 | 0.022 | 1.462 | |
| GRbaseCoverage-methods | 0.078 | 0.003 | 0.139 | |
| GRcoverage-methods | 0.140 | 0.004 | 0.221 | |
| GRcoverageSummit-methods | 0.068 | 0.002 | 0.111 | |
| GRenrichment-methods | 0.085 | 0.003 | 0.135 | |
| GRmidpoint-methods | 0.030 | 0.000 | 0.047 | |
| GRsetwidth | 0.042 | 0.001 | 0.069 | |
| TSS | 1.613 | 0.030 | 2.514 | |
| countOverlapsInBins-methods | 0.150 | 0.002 | 0.234 | |
| distanceFromTSS-methods | 2.490 | 0.055 | 3.901 | |
| enhancers | 0.487 | 0.016 | 0.759 | |
| findLncRNA | 0.822 | 0.025 | 1.302 | |
| getPromoterClass-methods | 1.962 | 0.045 | 33.987 | |
| heatmapData | 1.394 | 0.029 | 2.215 | |
| heatmapPlot | 3.404 | 0.166 | 5.375 | |
| makeGtfFromDb | 4.762 | 0.159 | 7.608 | |
| matchEnhancers | 2.145 | 0.045 | 3.290 | |
| overlapOfGRanges-methods | 0.066 | 0.001 | 0.085 | |
| palette2d | 0.052 | 0.003 | 0.067 | |
| plotStallingIndex | 3.002 | 0.060 | 4.315 | |
| simplifyGOterms | 0.527 | 0.084 | 0.864 | |
| stallingIndex | 2.879 | 0.053 | 3.699 | |
| topGOres | 40.566 | 1.009 | 62.815 | |
| ucsc2GRanges | 0.015 | 0.001 | 0.024 | |
| unionMaxScore-methods | 0.146 | 0.002 | 0.238 | |