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CHECK report for CAGEfightR on malbec2

This page was generated on 2020-10-17 11:54:31 -0400 (Sat, 17 Oct 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 218/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAGEfightR 1.8.0
Malte Thodberg
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/CAGEfightR
Branch: RELEASE_3_11
Last Commit: 224f1ab
Last Changed Date: 2020-04-27 15:16:40 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CAGEfightR
Version: 1.8.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:CAGEfightR.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings CAGEfightR_1.8.0.tar.gz
StartedAt: 2020-10-16 23:30:11 -0400 (Fri, 16 Oct 2020)
EndedAt: 2020-10-16 23:37:18 -0400 (Fri, 16 Oct 2020)
EllapsedTime: 427.0 seconds
RetCode: 0
Status:  OK 
CheckDir: CAGEfightR.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:CAGEfightR.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings CAGEfightR_1.8.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/CAGEfightR.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘1.8.0’
* 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    4.508  1.464   5.359
assignGeneID 4.846  0.039   5.795
* 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-3.11-bioc/R/bin/R CMD INSTALL CAGEfightR
###
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* installing to library ‘/home/biocbuild/bbs-3.11-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
assignGeneID4.8460.0395.795
assignMissingID1.5440.0001.543
assignTxID1.2610.0081.270
assignTxType0.0000.0000.001
balanceBC0.0010.0000.001
balanceD0.0010.0000.000
bwCommonGenome0.0670.0040.108
bwGenomeCompatibility0.0270.0000.027
bwValid0.0120.0000.012
calcBidirectionality0.7930.0000.793
calcComposition3.3420.0043.346
calcPooled0.1940.0000.193
calcShape4.6400.1724.812
calcSupport0.2450.0080.253
calcTPM0.2870.0080.295
calcTotalTags0.1210.0080.129
checkCTSSs0.4070.0000.417
checkPeaked0.0710.0120.082
checkPooled0.2060.0030.209
clusterBidirectionally000
clusterUnidirectionally1.4770.0001.477
combineClusters0.8680.0000.867
convertBAM2BigWig000
convertBED2BigWig0.0010.0000.000
convertGRanges2GPos0.0790.0000.078
exampleDesign0.0050.0000.006
findLinks4.5081.4645.359
findStretches0.6220.0440.666
quantifyCTSSs000
quantifyCTSSs20.0010.0000.001
quantifyClusters0.7380.0280.766
quantifyGenes1.2700.0521.322
quickEnhancers0.0010.0000.000
quickGenes000
quickTSSs000
shapeEntropy0.0010.0000.001
shapeIQR0.0010.0000.001
shapeMean0.0000.0000.001
shapeMultimodality000
subsetByBidirectionality0.4690.0130.483
subsetByComposition1.3760.0121.389
subsetBySupport0.0980.0000.098
swapRanges0.2680.0000.269
swapScores0.1510.0080.158
trackBalance0.0010.0000.000
trackCTSS4.0440.1724.216
trackClusters2.5720.0002.572
trackLinks1.0410.3741.194
trimToPeak0.9710.0641.040
trimToPercentiles3.1210.0043.125
tuneTagClustering0.0010.0000.000
utilsAggregateRows0.7450.1680.914
utilsDeStrand0.2200.0040.224
utilsScoreOverlaps0.1150.0000.114
utilsSimplifyTxDb0.0000.0000.001