Package: CAGEfightR

Version: 1.0.0

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_1.0.0.tar.gz

StartedAt: 2018-10-16 20:13:21 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 20:19:08 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 347.6 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_1.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/CAGEfightR.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.0.0’
* 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 6.023  0.212   6.323
trackBalance 5.691  0.037   5.759
* 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/3.5/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)

name	user	system	elapsed
assignGeneID	6.023	0.212	6.323
assignMissingID	2.342	0.069	2.427
assignTxID	1.282	0.056	1.348
assignTxType	0.005	0.000	0.006
bwCommonGenome	0.064	0.005	0.071
bwGenomeCompatibility	0.028	0.003	0.031
bwValid	0.011	0.002	0.013
calcBidirectionality	0.740	0.038	0.784
calcComposition	3.039	0.069	3.131
calcPooled	0.106	0.008	0.114
calcShape	4.503	0.085	4.603
calcSupport	0.097	0.009	0.105
calcTPM	0.143	0.009	0.153
calcTotalTags	0.066	0.008	0.075
clusterBidirectionally	0.002	0.000	0.002
clusterUnidirectionally	1.751	0.034	1.789
combineClusters	0.817	0.019	0.838
exampleDesign	0.010	0.008	0.018
quantifyCTSSs	0.003	0.000	0.003
quantifyClusters	0.502	0.044	0.549
quantifyGenes	2.560	0.067	2.663
quickEnhancers	0.001	0.000	0.000
quickTSSs	0.001	0.000	0.001
shapeEntropy	0.002	0.000	0.002
shapeIQR	0.002	0.000	0.002
shapeMultimodality	0.001	0.000	0.002
subsetByBidirectionality	0.422	0.027	0.452
subsetByComposition	2.580	0.058	2.650
subsetBySupport	0.071	0.002	0.073
swapRanges	0.241	0.019	0.263
swapScores	0.072	0.005	0.077
trackBalance	5.691	0.037	5.759
trackCTSS	1.519	0.023	1.559
trackClusters	1.773	0.013	1.796
trimToPeak	0.565	0.016	0.582
trimToPercentiles	1.786	0.074	1.867
tuneTagClustering	2.223	0.066	2.302