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BioC 3.6: CHECK report for epigenomix on malbec1

This page was generated on 2017-08-16 13:20:48 -0400 (Wed, 16 Aug 2017).

Package 412/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
epigenomix 1.17.1
Hans-Ulrich Klein
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/epigenomix
Last Changed Rev: 130713 / Revision: 131943
Last Changed Date: 2017-06-27 13:05:27 -0400 (Tue, 27 Jun 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

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

Command output

##############################################################################
##############################################################################
###
### 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

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-class0.0040.0000.001
MixModel-class000
MixModelBayes-class0.0000.0000.001
MixModelML-class000
MixtureComponent-class0.0040.0000.000
bayesMixModel18.976 0.04019.034
calculateCrossCorrelation1.1680.0041.171
eSet0.0480.0000.048
fpkm0.0320.0000.031
getAlignmentQuality000
integrateData0.20.00.2
mappedReads0.0320.0000.035
matchProbeToPromoter0.4600.0000.461
mlMixModel8.6800.0208.703
normalize0.1400.0000.142
normalizeChIP0.0360.0000.035
plotChains24.516 0.03224.564
plotClassification0.0280.0000.031
plotComponents0.0360.0000.039
summarizeReads0.4320.0000.432
transToTSS0.0000.0000.003