Package: CAGEfightR

Version: 1.6.0

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:CAGEfightR.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings CAGEfightR_1.6.0.tar.gz

StartedAt: 2020-04-15 05:45:32 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 05:51:29 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 356.6 seconds

RetCode: 0

Status:  OK

CheckDir: CAGEfightR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:CAGEfightR.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings CAGEfightR_1.6.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/CAGEfightR.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.6.0’
* 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
Examples with CPU or elapsed time > 5s
          user system elapsed
findLinks 4.28  1.312   5.169
* 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-3.10-bioc/R/bin/R CMD INSTALL CAGEfightR
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/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)

name	user	system	elapsed
assignGeneID	4.192	0.036	4.354
assignMissingID	1.568	0.024	1.595
assignTxID	1.296	0.012	1.310
assignTxType	0	0	0
balanceBC	0.000	0.000	0.001
balanceD	0	0	0
bwCommonGenome	0.06	0.00	0.09
bwGenomeCompatibility	0.02	0.00	0.02
bwValid	0.012	0.000	0.009
calcBidirectionality	0.888	0.000	0.888
calcComposition	3.108	0.024	3.138
calcPooled	0.204	0.020	0.225
calcShape	3.672	0.092	3.776
calcSupport	0.120	0.008	0.130
calcTPM	0.140	0.008	0.146
calcTotalTags	0.068	0.008	0.076
checkPeaked	0.080	0.000	0.078
checkPooled	0.072	0.008	0.081
clusterBidirectionally	0	0	0
clusterUnidirectionally	1.576	0.004	1.579
combineClusters	1.104	0.000	1.103
exampleDesign	0.000	0.008	0.008
findLinks	4.280	1.312	5.169
findStretches	0.572	0.024	0.593
quantifyCTSSs	0	0	0
quantifyClusters	0.764	0.040	0.855
quantifyGenes	1.672	0.040	1.716
quickEnhancers	0	0	0
quickTSSs	0	0	0
shapeEntropy	0.000	0.000	0.001
shapeIQR	0.000	0.000	0.001
shapeMultimodality	0	0	0
subsetByBidirectionality	0.572	0.004	0.577
subsetByComposition	1.724	0.000	1.723
subsetBySupport	0.132	0.008	0.138
swapRanges	0.344	0.008	0.352
swapScores	0.216	0.000	0.217
trackBalance	0	0	0
trackCTSS	3.600	0.104	3.721
trackClusters	2.524	0.000	2.554
trackLinks	1.084	0.352	1.253
trimToPeak	0.980	0.076	1.059
trimToPercentiles	2.760	0.024	2.796
tuneTagClustering	0	0	0