Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-21 13:07:28 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4079
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4140
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 machv2


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 235/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAGEfightR 1.14.0  (landing page)
Malte Thodberg
Snapshot Date: 2022-01-20 01:55:04 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/CAGEfightR
git_branch: RELEASE_3_14
git_last_commit: 6c27321
git_last_commit_date: 2021-10-26 12:44:41 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: CAGEfightR
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CAGEfightR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CAGEfightR_1.14.0.tar.gz
StartedAt: 2022-01-20 10:49:59 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 10:58:10 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 491.7 seconds
RetCode: 0
Status:   OK  
CheckDir: CAGEfightR.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CAGEfightR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CAGEfightR_1.14.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/CAGEfightR.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.14.0’
* 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
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
findLinks         6.117  1.540   6.117
assignGeneID      5.807  0.162   6.012
calcShape         5.532  0.238   5.775
trimToPercentiles 4.957  0.045   5.006
* 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

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CAGEfightR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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
assignGeneID5.8070.1626.012
assignMissingID3.0040.0793.085
assignTxID1.5990.0221.623
assignTxType0.0010.0010.001
balanceBC0.0000.0000.001
balanceD0.0010.0000.001
bwCommonGenome0.0570.0090.066
bwGenomeCompatibility0.0260.0060.032
bwValid0.0090.0030.012
calcBidirectionality0.7700.0280.798
calcComposition2.4330.0572.492
calcPooled0.2680.0060.275
calcShape5.5320.2385.775
calcSupport0.3140.0090.323
calcTPM0.2600.0040.264
calcTotalTags0.1160.0040.119
checkCTSSs0.4830.0050.491
checkPeaked0.1290.0050.134
checkPooled0.1980.0290.227
clusterBidirectionally0.0010.0000.001
clusterUnidirectionally2.6160.0372.656
combineClusters1.8090.0251.835
convertBAM2BigWig000
convertBED2BigWig0.0000.0010.001
convertGRanges2GPos0.1410.0000.142
exampleDesign0.0090.0120.020
findLinks6.1171.5406.117
findStretches0.9080.0880.997
quantifyCTSSs0.0010.0000.001
quantifyCTSSs20.0000.0000.001
quantifyClusters0.7690.0810.851
quantifyGenes2.5520.1322.685
quickEnhancers0.0000.0000.001
quickGenes0.0000.0010.000
quickTSSs0.0000.0000.001
shapeEntropy0.0010.0000.002
shapeIQR0.0000.0010.002
shapeMean0.0000.0010.002
shapeMultimodality000
subsetByBidirectionality1.0440.0271.074
subsetByComposition4.1190.2624.388
subsetBySupport0.3140.0050.321
swapRanges0.5520.0410.594
swapScores0.2920.0050.297
trackBalance0.0000.0010.002
trackCTSS4.6740.0684.747
trackClusters3.0480.0363.086
trackLinks2.0230.9522.034
trimToPeak1.9660.1842.152
trimToPercentiles4.9570.0455.006
tuneTagClustering0.0000.0000.001
utilsAggregateRows0.7150.6831.455
utilsDeStrand0.2410.0040.245
utilsScoreOverlaps0.1230.0000.124
utilsSimplifyTxDb0.0000.0010.001