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BioC 2.14: CHECK report for epigenomix on petty

This page was generated on 2014-10-08 09:00:46 -0700 (Wed, 08 Oct 2014).

Package 258/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
epigenomix 1.4.1
Hans-Ulrich Klein
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/epigenomix
Last Changed Rev: 89478 / Revision: 95116
Last Changed Date: 2014-04-25 06:27:30 -0700 (Fri, 25 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: epigenomix
Version: 1.4.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch epigenomix_1.4.1.tar.gz
StartedAt: 2014-10-07 21:50:08 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 22:01:05 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 657.1 seconds
RetCode: 0
Status:  OK 
CheckDir: epigenomix.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch epigenomix_1.4.1.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/epigenomix.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.4.1’
* 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 ... [26s/27s] 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 ... [364s/367s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
bayesMixModel 218.414 17.285 237.532
plotChains     79.021  0.179  79.540
mlMixModel     33.072  0.157  33.408
* 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

epigenomix.Rcheck/00install.out:

* 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)

epigenomix.Rcheck/epigenomix-Ex.timings:

nameusersystemelapsed
ChIPseqSet-class0.0040.0010.004
MixModel-class0.0020.0000.002
MixModelBayes-class0.0020.0000.002
MixModelML-class0.0020.0010.002
MixtureComponent-class0.0020.0000.002
bayesMixModel218.414 17.285237.532
eSet0.0680.0040.072
fpkm0.0600.0070.066
integrateData0.2800.0040.284
mappedReads0.1960.0020.197
matchProbeToPromoter1.0410.0071.050
mlMixModel33.072 0.15733.408
normalizeChIP0.0750.0010.076
plotChains79.021 0.17979.540
plotClassification0.0900.0020.096
plotComponents0.1220.0020.147
summarizeReads0.8080.0050.820
transToTSS0.0070.0000.024