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CHECK report for CAGEfightR on merida1

This page was generated on 2019-04-16 12:09:46 -0400 (Tue, 16 Apr 2019).

Package 190/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAGEfightR 1.2.0
Malte Thodberg
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/CAGEfightR
Branch: RELEASE_3_8
Last Commit: a324636
Last Changed Date: 2018-10-30 11:42:09 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: CAGEfightR
Version: 1.2.0
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_1.2.0.tar.gz
StartedAt: 2019-04-15 22:43:19 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 22:49:19 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 360.7 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_1.2.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/CAGEfightR.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.2.0’
* 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
* 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/3.5/Resources/library’
* installing *source* package ‘CAGEfightR’ ...
** 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
* DONE (CAGEfightR)

Tests output


Example timings

CAGEfightR.Rcheck/CAGEfightR-Ex.timings

nameusersystemelapsed
assignGeneID4.3890.1654.602
assignMissingID1.5560.0731.642
assignTxID1.4490.0611.581
assignTxType0.0010.0010.001
balanceBC0.0010.0000.001
balanceD0.0010.0010.001
bwCommonGenome0.0520.0040.058
bwGenomeCompatibility0.0250.0030.029
bwValid0.0070.0010.009
calcBidirectionality1.0250.0621.091
calcComposition2.6980.1002.809
calcPooled0.1110.0130.124
calcShape4.7190.0804.825
calcSupport0.1440.0110.155
calcTPM0.2150.0140.230
calcTotalTags0.0860.0040.092
checkPeaked0.0840.0070.090
checkPooled0.0620.0100.072
clusterBidirectionally0.0000.0000.001
clusterUnidirectionally2.1340.0412.187
combineClusters0.8780.0240.904
exampleDesign0.0100.0090.019
findLinks2.7071.0832.911
findStretches0.4940.0670.563
quantifyCTSSs0.0010.0010.001
quantifyClusters0.7650.1140.881
quantifyGenes1.7280.0931.836
quickEnhancers000
quickTSSs0.0000.0000.001
shapeEntropy0.0010.0000.001
shapeIQR0.0010.0010.001
shapeMultimodality000
subsetByBidirectionality0.5360.0500.591
subsetByComposition1.7310.0731.809
subsetBySupport0.0720.0040.076
swapRanges0.2310.0110.243
swapScores0.0980.0070.105
trackBalance0.0010.0000.001
trackCTSS3.8240.2484.098
trackClusters2.1800.0742.264
trackLinks1.3560.3711.475
trimToPeak0.9970.1531.154
trimToPercentiles2.4370.0882.542
tuneTagClustering0.0010.0000.001