Package: CAGEfightR

Version: 1.2.0

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:CAGEfightR.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings CAGEfightR_1.2.0.tar.gz

StartedAt: 2019-04-15 22:37:02 -0400 (Mon, 15 Apr 2019)

EndedAt: 2019-04-15 22:42:27 -0400 (Mon, 15 Apr 2019)

EllapsedTime: 325.4 seconds

RetCode: 0

Status:  OK

CheckDir: CAGEfightR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:CAGEfightR.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings CAGEfightR_1.2.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/CAGEfightR.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (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

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL CAGEfightR
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/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	3.784	0.040	3.826
assignMissingID	1.136	0.000	1.140
assignTxID	0.796	0.008	0.803
assignTxType	0	0	0
balanceBC	0.004	0.000	0.000
balanceD	0	0	0
bwCommonGenome	0.116	0.000	0.137
bwGenomeCompatibility	0.024	0.000	0.025
bwValid	0.012	0.000	0.011
calcBidirectionality	0.812	0.000	0.811
calcComposition	2.916	0.012	2.933
calcPooled	0.076	0.004	0.080
calcShape	4.612	0.028	4.652
calcSupport	0.156	0.000	0.160
calcTPM	0.184	0.016	0.200
calcTotalTags	0.092	0.012	0.106
checkPeaked	0.124	0.008	0.133
checkPooled	0.104	0.004	0.107
clusterBidirectionally	0	0	0
clusterUnidirectionally	2.468	0.004	2.472
combineClusters	1.068	0.000	1.069
exampleDesign	0.004	0.004	0.008
findLinks	2.400	0.824	2.856
findStretches	0.468	0.028	0.497
quantifyCTSSs	0.000	0.000	0.001
quantifyClusters	0.860	0.080	0.943
quantifyGenes	1.700	0.008	1.715
quickEnhancers	0	0	0
quickTSSs	0	0	0
shapeEntropy	0	0	0
shapeIQR	0	0	0
shapeMultimodality	0	0	0
subsetByBidirectionality	0.436	0.004	0.442
subsetByComposition	1.556	0.012	1.578
subsetBySupport	0.056	0.000	0.053
swapRanges	0.180	0.000	0.181
swapScores	0.080	0.000	0.077
trackBalance	0	0	0
trackCTSS	3.844	0.136	4.009
trackClusters	2.264	0.044	2.321
trackLinks	1.140	0.328	1.325
trimToPeak	0.712	0.096	0.811
trimToPercentiles	2.292	0.028	2.330
tuneTagClustering	0	0	0