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_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/CAGEfightR.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.4.0’
* 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    8.458  2.233   9.344
trackCTSS    4.906  0.695   5.604
assignGeneID 5.217  0.288   5.509
* 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	5.217	0.288	5.509
assignMissingID	1.872	0.139	2.019
assignTxID	1.531	0.090	1.622
assignTxType	0.001	0.001	0.002
balanceBC	0.001	0.000	0.001
balanceD	0.001	0.000	0.002
bwCommonGenome	0.067	0.007	0.078
bwGenomeCompatibility	0.029	0.004	0.034
bwValid	0.012	0.003	0.015
calcBidirectionality	1.082	0.097	1.181
calcComposition	3.428	0.151	3.580
calcPooled	0.124	0.017	0.141
calcShape	4.516	0.376	4.977
calcSupport	0.186	0.020	0.207
calcTPM	0.215	0.023	0.238
calcTotalTags	0.120	0.020	0.139
checkPeaked	0.154	0.016	0.171
checkPooled	0.138	0.032	0.171
clusterBidirectionally	0.000	0.001	0.001
clusterUnidirectionally	2.183	0.064	2.248
combineClusters	1.196	0.049	1.245
exampleDesign	0.012	0.016	0.029
findLinks	8.458	2.233	9.344
findStretches	0.673	0.131	0.804
quantifyCTSSs	0.001	0.001	0.001
quantifyClusters	0.780	0.184	0.964
quantifyGenes	1.718	0.178	1.897
quickEnhancers	0.001	0.001	0.000
quickTSSs	0	0	0
shapeEntropy	0.001	0.000	0.002
shapeIQR	0.001	0.000	0.001
shapeMultimodality	0.000	0.000	0.001
subsetByBidirectionality	0.673	0.099	0.771
subsetByComposition	2.106	0.201	2.308
subsetBySupport	0.121	0.004	0.125
swapRanges	0.217	0.024	0.239
swapScores	0.126	0.018	0.144
trackBalance	0.001	0.001	0.002
trackCTSS	4.906	0.695	5.604
trackClusters	2.761	0.069	2.832
trackLinks	3.378	0.835	3.617
trimToPeak	1.376	0.243	1.620
trimToPercentiles	3.054	0.208	3.272
tuneTagClustering	0.000	0.001	0.001

CHECK report for CAGEfightR on celaya2

Summary

Command output

Installation output

Tests output

Example timings