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BioC 3.1: CHECK report for epigenomix on morelia

This page was generated on 2015-10-09 09:40:48 -0700 (Fri, 09 Oct 2015).

Package 303/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
epigenomix 1.8.0
Hans-Ulrich Klein
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/epigenomix
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: epigenomix
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings epigenomix_1.8.0.tar.gz
StartedAt: 2015-10-09 01:39:09 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 01:43:58 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 288.3 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_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-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 ‘1.8.0’
* 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 ... [10s/12s] 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’
.calculateCrossCorrelation : <anonymous>: no visible global function
  definition for ‘Rle’
.getAlignmentQuality: no visible global function definition for
  ‘mclapply’
.summarizeReads: no visible global function definition for ‘DataFrame’
ChIPseqSet: no visible global function definition for ‘DataFrame’
ChIPseqSet: no visible global function definition for ‘SimpleList’
ChIPseqSet,matrix-GRanges: no visible global function definition for
  ‘DataFrame’
ChIPseqSet,matrix-GRanges: no visible global function definition for
  ‘SimpleList’
ChIPseqSet,matrix-GRangesList: no visible global function definition
  for ‘DataFrame’
ChIPseqSet,matrix-GRangesList: no visible global function definition
  for ‘SimpleList’
calculateCrossCorrelation,GRanges: no visible global function
  definition for ‘mclapply’
calculateCrossCorrelation,GRanges : <anonymous>: no visible global
  function definition for ‘keepSeqlevels’
calculateCrossCorrelation,GRanges : <anonymous>: no visible global
  function definition for ‘Rle’
getAlignmentQuality,character: no visible global function definition
  for ‘mclapply’
summarizeReads,GRangesList-GRanges-character: no visible global
  function definition for ‘DataFrame’
summarizeReads,GRangesList-GRangesList-character: no visible global
  function definition for ‘DataFrame’
* 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 ... [157s/157s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
bayesMixModel 97.767 11.060 108.856
plotChains    28.535  1.804  30.351
mlMixModel    10.095  0.656  10.755
* 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-3.1-bioc/meat/epigenomix.Rcheck/00check.log’
for details.


epigenomix.Rcheck/00install.out:

* installing *source* package ‘epigenomix’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (epigenomix)

epigenomix.Rcheck/epigenomix-Ex.timings:

nameusersystemelapsed
ChIPseqSet-class0.0020.0000.001
MixModel-class0.0010.0000.000
MixModelBayes-class0.0010.0000.001
MixModelML-class0.0000.0000.001
MixtureComponent-class0.0010.0000.000
bayesMixModel 97.767 11.060108.856
calculateCrossCorrelation0.5880.0110.599
eSet0.0100.0010.011
fpkm0.0280.0020.030
getAlignmentQuality0.0010.0000.001
integrateData0.0890.0020.091
mappedReads0.0380.0000.038
matchProbeToPromoter0.2170.0010.218
mlMixModel10.095 0.65610.755
normalizeChIP0.0250.0000.025
plotChains28.535 1.80430.351
plotClassification0.0270.0010.028
plotComponents0.0360.0000.038
summarizeReads0.1750.0010.175
transToTSS0.0060.0000.006