Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-01-21 11:05:36 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4163
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4058
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4000
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4117
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

CHECK results for CAGEfightR on nebbiolo1


To the developers/maintainers of the CAGEfightR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CAGEfightR.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 232/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAGEfightR 1.15.1  (landing page)
Malte Thodberg
Snapshot Date: 2022-01-20 13:55:17 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/CAGEfightR
git_branch: master
git_last_commit: aead2e0
git_last_commit_date: 2021-11-20 23:19:47 -0500 (Sat, 20 Nov 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'GenomicRanges' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: CAGEfightR
Version: 1.15.1
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:CAGEfightR.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings CAGEfightR_1.15.1.tar.gz
StartedAt: 2022-01-20 18:25:43 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 18:30:48 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 304.1 seconds
RetCode: 0
Status:   OK  
CheckDir: CAGEfightR.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:CAGEfightR.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings CAGEfightR_1.15.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/CAGEfightR.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CAGEfightR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CAGEfightR’ version ‘1.15.1’
* package encoding: UTF-8
* 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 ‘CAGEfightR’ 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 ... OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: OK


Installation output

CAGEfightR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL CAGEfightR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘CAGEfightR’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (CAGEfightR)

Tests output


Example timings

CAGEfightR.Rcheck/CAGEfightR-Ex.timings

nameusersystemelapsed
assignGeneID4.0970.0764.172
assignMissingID0.9720.0040.976
assignTxID0.7140.0120.726
assignTxType0.0000.0000.001
balanceBC0.0010.0000.000
balanceD0.0010.0000.000
bwCommonGenome0.0390.0000.046
bwGenomeCompatibility0.0150.0000.015
bwValid0.0070.0000.007
calcBidirectionality0.4530.0000.453
calcComposition1.1820.0001.183
calcPooled0.0880.0040.092
calcShape3.0010.0683.069
calcSupport0.1000.0000.099
calcTPM0.1080.0160.124
calcTotalTags0.0520.0120.064
checkCTSSs0.2130.0320.245
checkPeaked0.0540.0120.065
checkPooled0.1300.0040.134
clusterBidirectionally000
clusterUnidirectionally1.0960.0121.108
combineClusters0.6240.0040.628
convertBAM2BigWig0.0000.0000.001
convertBED2BigWig0.0000.0010.001
convertGRanges2GPos0.0620.0030.065
exampleDesign0.0050.0000.004
findLinks3.8250.8973.879
findStretches0.3190.0240.343
quantifyCTSSs0.0010.0000.001
quantifyCTSSs20.0000.0000.001
quantifyClusters0.3460.0320.378
quantifyGenes1.0470.0481.096
quickEnhancers0.0000.0000.001
quickGenes000
quickTSSs000
shapeEntropy000
shapeIQR000
shapeMean0.0010.0000.001
shapeMultimodality000
subsetByBidirectionality0.3320.0160.348
subsetByComposition1.0570.0121.069
subsetBySupport0.0710.0000.072
swapRanges0.2040.0000.204
swapScores0.0990.0040.104
trackBalance0.0000.0000.001
trackCTSS3.1830.0763.260
trackClusters2.0290.0002.029
trackLinks1.0760.5211.052
trimToPeak0.5850.0520.637
trimToPercentiles1.6120.0361.648
tuneTagClustering0.0010.0000.000
utilsAggregateRows0.3540.5200.873
utilsDeStrand0.1050.0000.106
utilsScoreOverlaps0.0550.0000.056
utilsSimplifyTxDb0.0010.0000.001