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CHECK report for CAGEfightR on merida1

This page was generated on 2020-04-15 12:47:26 -0400 (Wed, 15 Apr 2020).

Package 213/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAGEfightR 1.6.0
Malte Thodberg
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/CAGEfightR
Branch: RELEASE_3_10
Last Commit: a293b9a
Last Changed Date: 2019-10-29 13:11:11 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  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: 1.6.0
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_1.6.0.tar.gz
StartedAt: 2020-04-15 00:53:06 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 00:59:42 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 395.6 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_1.6.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/CAGEfightR.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.6.0’
* 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/3.6/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
assignGeneID4.5540.1644.811
assignMissingID1.6050.0601.674
assignTxID1.2040.0431.254
assignTxType0.0000.0000.001
balanceBC0.0010.0000.000
balanceD0.0010.0000.001
bwCommonGenome0.0540.0040.058
bwGenomeCompatibility0.0200.0020.022
bwValid0.0070.0010.009
calcBidirectionality0.9080.0500.966
calcComposition3.0300.0823.164
calcPooled0.2030.0240.227
calcShape3.8540.1814.043
calcSupport0.1820.0120.193
calcTPM0.2050.0130.219
calcTotalTags0.0730.0080.081
checkPeaked0.0810.0060.086
checkPooled0.1170.0180.135
clusterBidirectionally000
clusterUnidirectionally2.4530.0362.517
combineClusters1.2150.0301.253
exampleDesign0.0080.0080.018
findLinks4.3670.5604.514
findStretches0.5140.0670.584
quantifyCTSSs0.0000.0010.000
quantifyClusters0.7010.1020.805
quantifyGenes1.7000.1151.818
quickEnhancers000
quickTSSs000
shapeEntropy0.0010.0000.001
shapeIQR0.0010.0010.002
shapeMultimodality000
subsetByBidirectionality0.6800.0620.745
subsetByComposition1.7730.0811.857
subsetBySupport0.1330.0110.144
swapRanges0.3340.0120.346
swapScores0.1560.0060.163
trackBalance0.0010.0010.000
trackCTSS3.8780.2554.184
trackClusters2.3110.0672.384
trackLinks1.4700.2561.598
trimToPeak1.3870.1581.574
trimToPercentiles2.9500.0403.012
tuneTagClustering0.0010.0000.001