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CHECK report for CAGEfightR on malbec1

This page was generated on 2020-08-11 11:24:54 -0400 (Tue, 11 Aug 2020).

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 213/1885HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAGEfightR 1.9.0
Malte Thodberg
Snapshot Date: 2020-08-10 14:50:56 -0400 (Mon, 10 Aug 2020)
URL: https://git.bioconductor.org/packages/CAGEfightR
Branch: master
Last Commit: 4bec7db
Last Changed Date: 2020-04-27 15:16:40 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  NA 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CAGEfightR
Version: 1.9.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:CAGEfightR.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings CAGEfightR_1.9.0.tar.gz
StartedAt: 2020-08-11 04:08:51 -0400 (Tue, 11 Aug 2020)
EndedAt: 2020-08-11 04:15:12 -0400 (Tue, 11 Aug 2020)
EllapsedTime: 381.2 seconds
RetCode: 0
Status:  OK 
CheckDir: CAGEfightR.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:CAGEfightR.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings CAGEfightR_1.9.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/CAGEfightR.Rcheck’
* using R version 4.0.2 (2020-06-22)
* 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 ‘1.9.0’
* 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 4.244  1.132   4.933
* 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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###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL CAGEfightR
###
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* installing to library ‘/home/biocbuild/bbs-3.12-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
assignGeneID4.8960.0324.971
assignMissingID1.6200.0041.625
assignTxID1.0320.0121.048
assignTxType0.0000.0000.001
balanceBC0.0000.0000.001
balanceD0.0000.0000.001
bwCommonGenome0.0480.0040.159
bwGenomeCompatibility0.0240.0000.025
bwValid0.0120.0000.011
calcBidirectionality0.7040.0000.714
calcComposition2.0120.0042.018
calcPooled0.2000.0080.208
calcShape3.9600.0363.997
calcSupport0.2040.0040.208
calcTPM0.2640.0080.275
calcTotalTags0.1240.0000.125
checkCTSSs0.3880.0000.399
checkPeaked0.0760.0000.077
checkPooled0.0600.0040.065
clusterBidirectionally000
clusterUnidirectionally1.7400.0201.763
combineClusters1.0160.0001.016
convertBAM2BigWig000
convertBED2BigWig000
convertGRanges2GPos0.0800.0000.078
exampleDesign0.0040.0000.004
findLinks4.2441.1324.933
findStretches0.5360.0360.572
quantifyCTSSs000
quantifyCTSSs20.0040.0000.000
quantifyClusters0.4960.0480.544
quantifyGenes1.6720.0481.727
quickEnhancers000
quickGenes000
quickTSSs000
shapeEntropy0.0000.0000.001
shapeIQR0.0000.0040.002
shapeMean000
shapeMultimodality000
subsetByBidirectionality0.6120.0200.631
subsetByComposition1.5640.0041.571
subsetBySupport0.0960.0080.105
swapRanges0.2400.0080.247
swapScores0.1520.0000.150
trackBalance0.0000.0000.001
trackCTSS4.0840.1284.220
trackClusters2.6280.0002.630
trackLinks0.9800.3521.102
trimToPeak0.9200.0881.006
trimToPercentiles2.1760.0242.204
tuneTagClustering000
utilsAggregateRows0.4120.1200.535
utilsDeStrand0.1480.0000.148
utilsScoreOverlaps0.0680.0000.071
utilsSimplifyTxDb000