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CHECK report for CAGEfightR on celaya2

This page was generated on 2019-10-16 13:02:32 -0400 (Wed, 16 Oct 2019).

Package 200/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAGEfightR 1.4.0
Malte Thodberg
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/CAGEfightR
Branch: RELEASE_3_9
Last Commit: 90e6c25
Last Changed Date: 2019-05-02 11:54:12 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 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
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: CAGEfightR
Version: 1.4.0
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_1.4.0.tar.gz
StartedAt: 2019-10-16 01:05:15 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 01:13:25 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 490.2 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_1.4.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/CAGEfightR.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.4.0’
* 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 or elapsed time > 5s
              user system elapsed
findLinks    8.458  2.233   9.344
trackCTSS    4.906  0.695   5.604
assignGeneID 5.217  0.288   5.509
* 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/3.6/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
assignGeneID5.2170.2885.509
assignMissingID1.8720.1392.019
assignTxID1.5310.0901.622
assignTxType0.0010.0010.002
balanceBC0.0010.0000.001
balanceD0.0010.0000.002
bwCommonGenome0.0670.0070.078
bwGenomeCompatibility0.0290.0040.034
bwValid0.0120.0030.015
calcBidirectionality1.0820.0971.181
calcComposition3.4280.1513.580
calcPooled0.1240.0170.141
calcShape4.5160.3764.977
calcSupport0.1860.0200.207
calcTPM0.2150.0230.238
calcTotalTags0.1200.0200.139
checkPeaked0.1540.0160.171
checkPooled0.1380.0320.171
clusterBidirectionally0.0000.0010.001
clusterUnidirectionally2.1830.0642.248
combineClusters1.1960.0491.245
exampleDesign0.0120.0160.029
findLinks8.4582.2339.344
findStretches0.6730.1310.804
quantifyCTSSs0.0010.0010.001
quantifyClusters0.7800.1840.964
quantifyGenes1.7180.1781.897
quickEnhancers0.0010.0010.000
quickTSSs000
shapeEntropy0.0010.0000.002
shapeIQR0.0010.0000.001
shapeMultimodality0.0000.0000.001
subsetByBidirectionality0.6730.0990.771
subsetByComposition2.1060.2012.308
subsetBySupport0.1210.0040.125
swapRanges0.2170.0240.239
swapScores0.1260.0180.144
trackBalance0.0010.0010.002
trackCTSS4.9060.6955.604
trackClusters2.7610.0692.832
trackLinks3.3780.8353.617
trimToPeak1.3760.2431.620
trimToPercentiles3.0540.2083.272
tuneTagClustering0.0000.0010.001