Multiple platform build/check report for BioC 3.11 - CHECK report for epigenomix on machv2

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:epigenomix.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings epigenomix_1.28.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/epigenomix.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘epigenomix/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘epigenomix’ version ‘1.28.0’
* 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 ‘epigenomix’ 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
plotChains    42.490  0.348  42.925
bayesMixModel 33.592  0.279  33.941
mlMixModel    18.926  0.232  19.238
* 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 epigenomix
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘epigenomix’ ...
** using staged installation
** R
** data
** 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 (epigenomix)

Tests output

Example timings

name	user	system	elapsed
ChIPseqSet-class	0.002	0.001	0.003
MixModel-class	0.001	0.000	0.001
MixModelBayes-class	0.001	0.000	0.001
MixModelML-class	0.001	0.000	0.002
MixtureComponent-class	0.000	0.000	0.001
bayesMixModel	33.592	0.279	33.941
calculateCrossCorrelation	1.276	0.006	1.283
eSet	0.020	0.003	0.023
fpkm	0.050	0.005	0.054
getAlignmentQuality	0	0	0
integrateData	0.259	0.003	0.261
mappedReads	0.053	0.003	0.056
matchProbeToPromoter	0.523	0.006	0.531
mlMixModel	18.926	0.232	19.238
normalize	0.261	0.001	0.262
normalizeChIP	0.172	0.002	0.173
plotChains	42.490	0.348	42.925
plotClassification	0.057	0.002	0.060
plotComponents	0.071	0.004	0.075
summarizeReads	0.444	0.001	0.446
transToTSS	0.003	0.003	0.007

CHECK report for epigenomix on machv2

Summary

Command output

Installation output

Tests output

Example timings