Package: epigenomix

Version: 1.18.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings epigenomix_1.18.0.tar.gz

StartedAt: 2018-04-11 23:14:56 -0400 (Wed, 11 Apr 2018)

EndedAt: 2018-04-11 23:18:36 -0400 (Wed, 11 Apr 2018)

EllapsedTime: 220.2 seconds

RetCode: 0

Status:  OK

CheckDir: epigenomix.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings epigenomix_1.18.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/epigenomix.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (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 ‘1.18.0’
* 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 loading without being on the library search path ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
plotChains    27.408  0.012  27.450
bayesMixModel 19.216  0.060  19.294
mlMixModel    10.072  0.016  10.098
* 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

* installing *source* package ‘epigenomix’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (epigenomix)

name	user	system	elapsed
ChIPseqSet-class	0.000	0.000	0.001
MixModel-class	0.000	0.000	0.001
MixModelBayes-class	0.004	0.000	0.000
MixModelML-class	0.000	0.000	0.001
MixtureComponent-class	0	0	0
bayesMixModel	19.216	0.060	19.294
calculateCrossCorrelation	1.168	0.000	1.168
eSet	0.044	0.000	0.045
fpkm	0.024	0.004	0.031
getAlignmentQuality	0	0	0
integrateData	0.200	0.000	0.201
mappedReads	0.052	0.000	0.052
matchProbeToPromoter	0.488	0.000	0.487
mlMixModel	10.072	0.016	10.098
normalize	0.140	0.000	0.138
normalizeChIP	0.036	0.000	0.034
plotChains	27.408	0.012	27.450
plotClassification	0.032	0.000	0.032
plotComponents	0.044	0.000	0.043
summarizeReads	0.472	0.000	0.471
transToTSS	0.004	0.000	0.002