Package: CAGEfightR

Version: 1.3.0

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_1.3.0.tar.gz

StartedAt: 2019-04-08 23:37:47 -0400 (Mon, 08 Apr 2019)

EndedAt: 2019-04-08 23:43:40 -0400 (Mon, 08 Apr 2019)

EllapsedTime: 353.0 seconds

RetCode: 0

Status:  OK

CheckDir: CAGEfightR.Rcheck

Warnings: 0

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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_1.3.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/CAGEfightR.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘1.3.0’
* 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
assignGeneID 4.851   0.15   5.057
* 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

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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’ ...
** 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)

name	user	system	elapsed
assignGeneID	4.851	0.150	5.057
assignMissingID	1.337	0.066	1.409
assignTxID	1.141	0.052	1.198
assignTxType	0.000	0.000	0.001
balanceBC	0.001	0.000	0.000
balanceD	0.001	0.001	0.001
bwCommonGenome	0.047	0.003	0.050
bwGenomeCompatibility	0.017	0.003	0.020
bwValid	0.007	0.001	0.008
calcBidirectionality	0.750	0.044	0.799
calcComposition	2.635	0.071	2.723
calcPooled	0.104	0.016	0.120
calcShape	3.408	0.078	3.500
calcSupport	0.160	0.011	0.171
calcTPM	0.181	0.006	0.189
calcTotalTags	0.098	0.010	0.107
checkPeaked	0.089	0.006	0.096
checkPooled	0.073	0.011	0.084
clusterBidirectionally	0.001	0.000	0.001
clusterUnidirectionally	1.984	0.038	2.036
combineClusters	0.908	0.022	0.941
exampleDesign	0.010	0.008	0.019
findLinks	2.559	0.928	2.634
findStretches	0.493	0.075	0.570
quantifyCTSSs	0.000	0.000	0.001
quantifyClusters	0.618	0.081	0.702
quantifyGenes	1.539	0.098	1.642
quickEnhancers	0	0	0
quickTSSs	0.000	0.000	0.001
shapeEntropy	0.001	0.000	0.001
shapeIQR	0.001	0.000	0.001
shapeMultimodality	0	0	0
subsetByBidirectionality	0.487	0.044	0.533
subsetByComposition	1.658	0.069	1.733
subsetBySupport	0.107	0.003	0.112
swapRanges	0.217	0.011	0.230
swapScores	0.085	0.005	0.090
trackBalance	0	0	0
trackCTSS	3.511	0.220	3.759
trackClusters	2.051	0.074	2.134
trackLinks	1.432	0.412	1.537
trimToPeak	0.934	0.122	1.059
trimToPercentiles	2.307	0.128	2.449
tuneTagClustering	0.001	0.000	0.000