BioC 3.5: CHECK report for epigenomix on toluca2

Package: epigenomix

Version: 1.15.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings epigenomix_1.15.1.tar.gz

StartedAt: 2017-04-23 03:30:23 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 03:35:46 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 323.1 seconds

RetCode: 0

Status:  OK

CheckDir: epigenomix.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings epigenomix_1.15.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/epigenomix.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.15.1’
* 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 sizes of PDF files under ‘inst/doc’ ... 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    37.759  0.335  38.235
bayesMixModel 31.618  0.287  32.138
mlMixModel    16.241  0.204  16.591
* 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	0.003	0.000	0.003
MixModel-class	0.002	0.000	0.002
MixModelBayes-class	0.001	0.000	0.001
MixModelML-class	0.001	0.000	0.001
MixtureComponent-class	0.000	0.000	0.001
bayesMixModel	31.618	0.287	32.138
calculateCrossCorrelation	1.975	0.011	1.995
eSet	0.084	0.002	0.086
fpkm	0.042	0.005	0.047
getAlignmentQuality	0	0	0
integrateData	0.316	0.001	0.320
mappedReads	0.074	0.002	0.077
matchProbeToPromoter	0.795	0.002	0.799
mlMixModel	16.241	0.204	16.591
normalize	0.231	0.001	0.233
normalizeChIP	0.052	0.000	0.053
plotChains	37.759	0.335	38.235
plotClassification	0.037	0.001	0.039
plotComponents	0.061	0.001	0.062
summarizeReads	0.694	0.001	0.696
transToTSS	0.004	0.001	0.005