BioC 3.6: CHECK report for epigenomix on malbec1

Package: epigenomix

Version: 1.17.1

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings epigenomix_1.17.1.tar.gz

StartedAt: 2017-08-15 22:55:14 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 22:58:56 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 222.4 seconds

RetCode: 0

Status:  OK

CheckDir: epigenomix.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings epigenomix_1.17.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/epigenomix.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.17.1’
* 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    24.516  0.032  24.564
bayesMixModel 18.976  0.040  19.034
mlMixModel     8.680  0.020   8.703
* 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	0.004	0.000	0.001
MixModel-class	0	0	0
MixModelBayes-class	0.000	0.000	0.001
MixModelML-class	0	0	0
MixtureComponent-class	0.004	0.000	0.000
bayesMixModel	18.976	0.040	19.034
calculateCrossCorrelation	1.168	0.004	1.171
eSet	0.048	0.000	0.048
fpkm	0.032	0.000	0.031
getAlignmentQuality	0	0	0
integrateData	0.2	0.0	0.2
mappedReads	0.032	0.000	0.035
matchProbeToPromoter	0.460	0.000	0.461
mlMixModel	8.680	0.020	8.703
normalize	0.140	0.000	0.142
normalizeChIP	0.036	0.000	0.035
plotChains	24.516	0.032	24.564
plotClassification	0.028	0.000	0.031
plotComponents	0.036	0.000	0.039
summarizeReads	0.432	0.000	0.432
transToTSS	0.000	0.000	0.003