Package: CAGEfightR

Version: 1.0.0

Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:CAGEfightR.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings CAGEfightR_1.0.0.tar.gz

StartedAt: 2018-10-15 22:56:18 -0400 (Mon, 15 Oct 2018)

EndedAt: 2018-10-15 23:00:27 -0400 (Mon, 15 Oct 2018)

EllapsedTime: 248.8 seconds

RetCode: 0

Status:  OK

CheckDir: CAGEfightR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:CAGEfightR.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings CAGEfightR_1.0.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/CAGEfightR.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.0.0’
* 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 4.648  0.028   5.043
* 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-3.7-bioc/R/bin/R CMD INSTALL CAGEfightR
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* installing to library ‘/home/biocbuild/bbs-3.7-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	4.648	0.028	5.043
assignMissingID	1.332	0.012	1.344
assignTxID	0.732	0.008	0.741
assignTxType	0.004	0.000	0.002
bwCommonGenome	0.052	0.000	0.160
bwGenomeCompatibility	0.028	0.000	0.027
bwValid	0.012	0.000	0.011
calcBidirectionality	0.476	0.000	0.494
calcComposition	2.416	0.008	2.427
calcPooled	0.056	0.012	0.071
calcShape	2.196	0.028	2.227
calcSupport	0.124	0.000	0.123
calcTPM	0.168	0.012	0.177
calcTotalTags	0.092	0.000	0.093
clusterBidirectionally	0.000	0.000	0.001
clusterUnidirectionally	1.472	0.008	1.484
combineClusters	0.744	0.012	0.758
exampleDesign	0.000	0.004	0.006
quantifyCTSSs	0.004	0.000	0.001
quantifyClusters	0.336	0.004	0.342
quantifyGenes	1.372	0.008	1.383
quickEnhancers	0.004	0.000	0.000
quickTSSs	0	0	0
shapeEntropy	0.000	0.000	0.001
shapeIQR	0.004	0.000	0.001
shapeMultimodality	0	0	0
subsetByBidirectionality	0.300	0.000	0.297
subsetByComposition	1.628	0.000	1.629
subsetBySupport	0.048	0.000	0.049
swapRanges	0.108	0.000	0.111
swapScores	0.048	0.000	0.050
trackBalance	4.284	0.004	4.324
trackCTSS	0.968	0.000	0.970
trackClusters	1.392	0.000	1.394
trimToPeak	0.396	0.000	0.395
trimToPercentiles	1.244	0.004	1.248
tuneTagClustering	2.320	0.164	2.507