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BioC 3.2: CHECK report for epigenomix on oaxaca

This page was generated on 2015-08-24 10:57:30 -0700 (Mon, 24 Aug 2015).

Package 313/1071HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
epigenomix 1.9.2
Hans-Ulrich Klein
Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/epigenomix
Last Changed Rev: 105144 / Revision: 107696
Last Changed Date: 2015-06-18 19:12:23 -0700 (Thu, 18 Jun 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: epigenomix
Version: 1.9.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings epigenomix_1.9.2.tar.gz
StartedAt: 2015-08-23 23:38:08 -0700 (Sun, 23 Aug 2015)
EndedAt: 2015-08-23 23:44:28 -0700 (Sun, 23 Aug 2015)
EllapsedTime: 380.0 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 epigenomix_1.9.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/epigenomix.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.9.2’
* 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 ... [17s/19s] 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 ... NOTE
.calculateCrossCorrelation: no visible global function definition for
  ‘mclapply’
.calculateCrossCorrelation : <anonymous>: no visible global function
  definition for ‘keepSeqlevels’
.getAlignmentQuality: no visible global function definition for
  ‘mclapply’
calculateCrossCorrelation,GRanges: no visible global function
  definition for ‘mclapply’
calculateCrossCorrelation,GRanges : <anonymous>: no visible global
  function definition for ‘keepSeqlevels’
getAlignmentQuality,character: no visible global function definition
  for ‘mclapply’
* 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 ... [191s/192s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
bayesMixModel 118.604  8.023 126.787
plotChains     38.161  0.508  38.832
mlMixModel     14.737  0.217  14.966
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/epigenomix.Rcheck/00check.log’
for details.


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-class0.0020.0000.002
MixModel-class0.0020.0000.001
MixModelBayes-class0.0010.0000.002
MixModelML-class0.0010.0000.002
MixtureComponent-class0.0010.0000.001
bayesMixModel118.604 8.023126.787
calculateCrossCorrelation1.0630.0311.095
eSet0.0150.0000.016
fpkm0.0420.0050.047
getAlignmentQuality000
integrateData0.1810.0010.182
mappedReads0.0570.0010.057
matchProbeToPromoter0.3450.0020.348
mlMixModel14.737 0.21714.966
normalizeChIP0.0620.0010.063
plotChains38.161 0.50838.832
plotClassification0.0460.0010.046
plotComponents0.0640.0010.065
summarizeReads0.2830.0010.284
transToTSS0.0040.0010.005