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CHECK report for CAGEfightR on merida1

This page was generated on 2021-05-06 12:34:28 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the CAGEfightR package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 223/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAGEfightR 1.10.0  (landing page)
Malte Thodberg
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/CAGEfightR
Branch: RELEASE_3_12
Last Commit: 2ed5872
Last Changed Date: 2020-10-27 11:35:28 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: CAGEfightR
Version: 1.10.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CAGEfightR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CAGEfightR_1.10.0.tar.gz
StartedAt: 2021-05-05 23:53:43 -0400 (Wed, 05 May 2021)
EndedAt: 2021-05-06 00:01:03 -0400 (Thu, 06 May 2021)
EllapsedTime: 439.7 seconds
RetCode: 0
Status:   OK  
CheckDir: CAGEfightR.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CAGEfightR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CAGEfightR_1.10.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/CAGEfightR.Rcheck’
* using R version 4.0.5 (2021-03-31)
* 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 ‘1.10.0’
* 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 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 4.615  1.144   4.654
calcShape 5.315  0.109   5.462
* 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:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CAGEfightR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/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
assignGeneID4.8070.1454.995
assignMissingID1.5560.0321.590
assignTxID1.4610.0221.484
assignTxType0.0010.0010.002
balanceBC0.0010.0000.001
balanceD0.0000.0000.001
bwCommonGenome0.0660.0060.072
bwGenomeCompatibility0.0300.0040.034
bwValid0.0120.0040.016
calcBidirectionality0.8320.0190.851
calcComposition2.4000.0352.436
calcPooled0.2130.0060.219
calcShape5.3150.1095.462
calcSupport0.1900.0030.193
calcTPM0.1930.0060.200
calcTotalTags0.0840.0020.086
checkCTSSs0.2950.0040.300
checkPeaked0.0960.0040.099
checkPooled0.0920.0030.093
clusterBidirectionally0.0000.0000.001
clusterUnidirectionally2.0990.0252.127
combineClusters1.0290.0131.042
convertBAM2BigWig000
convertBED2BigWig0.0010.0000.001
convertGRanges2GPos0.0950.0000.096
exampleDesign0.0060.0090.015
findLinks4.6151.1444.654
findStretches0.6510.2000.853
quantifyCTSSs0.0010.0010.002
quantifyCTSSs20.0000.0010.001
quantifyClusters0.8050.3260.873
quantifyGenes1.6370.0911.729
quickEnhancers000
quickGenes0.0010.0000.001
quickTSSs0.0000.0000.001
shapeEntropy0.0010.0010.001
shapeIQR0.0000.0010.001
shapeMean0.0010.0000.001
shapeMultimodality000
subsetByBidirectionality0.5980.0360.634
subsetByComposition1.7010.0471.750
subsetBySupport0.1100.0030.112
swapRanges0.2530.0100.263
swapScores0.1790.0120.192
trackBalance0.0010.0000.001
trackCTSS3.3420.1733.520
trackClusters2.1790.0352.221
trackLinks1.5530.7991.570
trimToPeak1.3290.1581.493
trimToPercentiles3.7540.0753.842
tuneTagClustering0.0010.0010.002
utilsAggregateRows0.8990.7181.663
utilsDeStrand0.2560.0060.263
utilsScoreOverlaps0.1270.0020.130
utilsSimplifyTxDb000