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BioC 2.12: CHECK report for epigenomix on petty

This page was generated on 2013-10-09 09:40:20 -0700 (Wed, 09 Oct 2013).

Package 207/671HostnameOS / ArchBUILDCHECKBUILD BIN
epigenomix 1.0.1
Hans-Ulrich Klein
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/epigenomix
Last Changed Rev: 75868 / Revision: 81334
Last Changed Date: 2013-04-22 06:50:33 -0700 (Mon, 22 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: epigenomix
Version: 1.0.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch epigenomix_1.0.1.tar.gz
StartedAt: 2013-10-08 22:16:23 -0700 (Tue, 08 Oct 2013)
EndedAt: 2013-10-08 22:23:38 -0700 (Tue, 08 Oct 2013)
EllapsedTime: 434.8 seconds
RetCode: 0
Status:  OK 
CheckDir: epigenomix.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/epigenomix.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'epigenomix/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'epigenomix' version '1.0.1'
* 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 ... [23s/23s] OK
* checking installed package size ... OK
* checking package 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 for unstated 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 examples ... [197s/199s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
plotChains    79.457  0.198  80.319
bayesMixModel 63.804  0.317  64.727
mlMixModel    38.630  0.111  39.085
* 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 vignettes ... 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-class0.0110.0020.013
MixModel-class0.0100.0010.010
MixModelBayes-class0.0120.0010.013
MixModelML-class0.0130.0010.013
MixtureComponent-class0.0100.0020.011
bayesMixModel63.804 0.31764.727
eSet0.0680.0050.073
integrateData0.2960.0030.302
mappedReads0.1680.0040.174
matchProbeToPromoter0.8440.0050.858
mlMixModel38.630 0.11139.085
normalizeChIP0.0780.0020.081
plotChains79.457 0.19880.319
plotClassification0.1090.0030.115
plotComponents0.1520.0040.159
summarizeReads0.7690.0030.777
transToTSS0.0170.0020.019