Package: CAGEfightR

Version: 1.4.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:CAGEfightR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings CAGEfightR_1.4.0.tar.gz

StartedAt: 2019-10-16 00:13:26 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 00:19:04 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 338.6 seconds

RetCode: 0

Status:  OK

CheckDir: CAGEfightR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:CAGEfightR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings CAGEfightR_1.4.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/CAGEfightR.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.4.0’
* 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 6.231  1.655   7.318
* 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-3.9-bioc/R/bin/R CMD INSTALL CAGEfightR
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* installing to library ‘/home/biocbuild/bbs-3.9-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	3.510	0.031	3.542
assignMissingID	1.587	0.007	1.595
assignTxID	1.308	0.008	1.316
assignTxType	0.001	0.000	0.000
balanceBC	0.001	0.000	0.001
balanceD	0.001	0.000	0.000
bwCommonGenome	0.104	0.000	0.137
bwGenomeCompatibility	0.019	0.000	0.020
bwValid	0.006	0.004	0.009
calcBidirectionality	0.801	0.004	0.825
calcComposition	2.797	0.020	2.817
calcPooled	0.099	0.004	0.103
calcShape	2.705	0.108	2.813
calcSupport	0.155	0.004	0.159
calcTPM	0.147	0.012	0.159
calcTotalTags	0.089	0.016	0.104
checkPeaked	0.114	0.008	0.122
checkPooled	0.058	0.008	0.067
clusterBidirectionally	0	0	0
clusterUnidirectionally	1.367	0.000	1.367
combineClusters	0.615	0.004	0.618
exampleDesign	0.005	0.000	0.005
findLinks	6.231	1.655	7.318
findStretches	0.342	0.068	0.307
quantifyCTSSs	0	0	0
quantifyClusters	0.415	0.020	0.434
quantifyGenes	1.023	0.020	1.043
quickEnhancers	0	0	0
quickTSSs	0	0	0
shapeEntropy	0.001	0.000	0.001
shapeIQR	0.001	0.000	0.001
shapeMultimodality	0	0	0
subsetByBidirectionality	0.376	0.011	0.387
subsetByComposition	1.810	0.008	1.818
subsetBySupport	0.104	0.000	0.104
swapRanges	0.249	0.000	0.249
swapScores	0.104	0.004	0.108
trackBalance	0	0	0
trackCTSS	2.974	0.152	3.126
trackClusters	1.709	0.024	1.733
trackLinks	1.953	0.423	2.035
trimToPeak	0.509	0.048	0.557
trimToPercentiles	1.486	0.048	1.535
tuneTagClustering	0.000	0.000	0.001