| Back to Multiple platform build/check report for BioC 3.17 |
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This page was generated on 2023-04-12 10:55:35 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | 4.3.0 alpha (2023-04-03 r84154) | 4547 |
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" | 4333 |
| 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: - 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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 406/2207 | 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 | |||||||||
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | WARNINGS | ||||||||||
| Package: compEpiTools |
| Version: 1.33.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:compEpiTools.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings compEpiTools_1.33.0.tar.gz |
| StartedAt: 2023-04-12 05:29:41 -0400 (Wed, 12 Apr 2023) |
| EndedAt: 2023-04-12 05:37:37 -0400 (Wed, 12 Apr 2023) |
| EllapsedTime: 475.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: compEpiTools.Rcheck |
| Warnings: 1 |
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### Running command:
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### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:compEpiTools.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings compEpiTools_1.33.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/compEpiTools.Rcheck’
* using R Under development (unstable) (2023-02-14 r83833)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
* running under: Ubuntu 20.04.6 LTS
* using session charset: UTF-8
* 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 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 ... 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 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 28.634 0.336 28.971
getPromoterClass-methods 0.760 0.020 18.326
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘compEpiTools.rnw’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 1 NOTE
See
‘/home/biocbuild/bbs-3.17-bioc/meat/compEpiTools.Rcheck/00check.log’
for details.
compEpiTools.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL compEpiTools ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-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 | 0.423 | 0.016 | 0.439 | |
| GRanges2ucsc-methods | 0.009 | 0.000 | 0.009 | |
| GRangesInPromoters-methods | 1.904 | 0.084 | 1.988 | |
| GRannotate-methods | 4.742 | 0.072 | 4.814 | |
| GRannotateSimple | 0.510 | 0.008 | 0.517 | |
| GRbaseCoverage-methods | 0.059 | 0.000 | 0.059 | |
| GRcoverage-methods | 0.110 | 0.004 | 0.114 | |
| GRcoverageSummit-methods | 0.054 | 0.000 | 0.054 | |
| GRenrichment-methods | 0.066 | 0.000 | 0.066 | |
| GRmidpoint-methods | 0.025 | 0.000 | 0.025 | |
| GRsetwidth | 0.030 | 0.008 | 0.038 | |
| TSS | 1.118 | 0.088 | 1.206 | |
| countOverlapsInBins-methods | 0.108 | 0.004 | 0.112 | |
| distanceFromTSS-methods | 1.695 | 0.028 | 1.725 | |
| enhancers | 0.345 | 0.000 | 0.345 | |
| findLncRNA | 0.644 | 0.007 | 0.654 | |
| getPromoterClass-methods | 0.760 | 0.020 | 18.326 | |
| heatmapData | 0.888 | 0.029 | 0.916 | |
| heatmapPlot | 2.490 | 0.019 | 2.510 | |
| makeGtfFromDb | 2.935 | 0.080 | 3.015 | |
| matchEnhancers | 1.655 | 0.004 | 1.660 | |
| overlapOfGRanges-methods | 0.05 | 0.00 | 0.05 | |
| palette2d | 0.046 | 0.000 | 0.045 | |
| plotStallingIndex | 2.255 | 0.008 | 2.265 | |
| simplifyGOterms | 0.403 | 0.057 | 0.580 | |
| stallingIndex | 2.263 | 0.020 | 2.283 | |
| topGOres | 28.634 | 0.336 | 28.971 | |
| ucsc2GRanges | 0.013 | 0.000 | 0.013 | |
| unionMaxScore-methods | 0.111 | 0.000 | 0.111 | |