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BioC 3.0: CHECK report for epigenomix on oaxaca

This page was generated on 2015-04-10 10:06:59 -0700 (Fri, 10 Apr 2015).

Package 278/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
epigenomix 1.6.0
Hans-Ulrich Klein
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/epigenomix
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 

Summary

Package: epigenomix
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch epigenomix_1.6.0.tar.gz
StartedAt: 2015-04-09 23:14:07 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 23:21:21 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 434.7 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_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/epigenomix.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘1.6.0’
* 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 ... [19s/24s] 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 ... [219s/220s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
bayesMixModel 135.031  8.607 144.144
plotChains     44.998  0.502  45.621
mlMixModel     18.358  0.214  18.860
* 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

NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-3.0-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-class0.0030.0000.003
MixModel-class0.0020.0010.001
MixModelBayes-class0.0010.0000.001
MixModelML-class0.0010.0000.001
MixtureComponent-class0.0010.0000.001
bayesMixModel135.031 8.607144.144
calculateCrossCorrelation0.9050.0090.914
eSet0.0290.0020.030
fpkm0.0420.0050.046
getAlignmentQuality0.0010.0000.000
integrateData0.1380.0010.138
mappedReads0.0520.0010.052
matchProbeToPromoter0.3510.0040.355
mlMixModel18.358 0.21418.860
normalizeChIP0.0450.0010.046
plotChains44.998 0.50245.621
plotClassification0.0330.0000.035
plotComponents0.0440.0010.044
summarizeReads0.2870.0010.288
transToTSS0.0030.0010.004