Multiple platform build/check report for BioC 3.9 - CHECK report for CAGEfightR on celaya2

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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_1.3.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/CAGEfightR.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.3.0’
* 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 5.38  0.324   5.801
findLinks    3.64  1.839   4.006
* 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

Installation output

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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/3.6/Resources/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)

Tests output

Example timings

name	user	system	elapsed
assignGeneID	5.380	0.324	5.801
assignMissingID	1.687	0.117	1.839
assignTxID	1.502	0.096	1.598
assignTxType	0.001	0.001	0.002
balanceBC	0.001	0.000	0.002
balanceD	0.001	0.000	0.002
bwCommonGenome	0.171	0.018	0.194
bwGenomeCompatibility	0.028	0.003	0.031
bwValid	0.012	0.005	0.016
calcBidirectionality	0.915	0.081	0.997
calcComposition	3.242	0.133	3.377
calcPooled	0.150	0.028	0.178
calcShape	4.328	0.192	4.521
calcSupport	0.133	0.014	0.147
calcTPM	0.197	0.020	0.217
calcTotalTags	0.139	0.021	0.160
checkPeaked	0.115	0.003	0.118
checkPooled	0.082	0.018	0.101
clusterBidirectionally	0.001	0.000	0.002
clusterUnidirectionally	2.243	0.075	2.318
combineClusters	1.166	0.052	1.219
exampleDesign	0.015	0.018	0.033
findLinks	3.640	1.839	4.006
findStretches	0.798	0.149	0.948
quantifyCTSSs	0.001	0.000	0.001
quantifyClusters	0.886	0.189	1.074
quantifyGenes	2.316	0.285	2.648
quickEnhancers	0	0	0
quickTSSs	0.000	0.000	0.001
shapeEntropy	0.000	0.001	0.001
shapeIQR	0.001	0.001	0.001
shapeMultimodality	0.001	0.001	0.000
subsetByBidirectionality	0.623	0.100	0.723
subsetByComposition	1.949	0.145	2.095
subsetBySupport	0.089	0.003	0.092
swapRanges	0.193	0.016	0.209
swapScores	1.418	0.428	1.845
trackBalance	0.001	0.001	0.001
trackCTSS	3.945	0.135	4.082
trackClusters	2.667	0.095	2.763
trackLinks	2.218	0.795	2.452
trimToPeak	1.375	0.256	1.630
trimToPercentiles	2.822	0.266	3.089
tuneTagClustering	0.000	0.001	0.001

CHECK report for CAGEfightR on celaya2

Summary

Command output

Installation output

Tests output

Example timings