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BioC experimental data: CHECK report for Fletcher2013b on perceval

This page was generated on 2015-04-08 17:41:38 -0700 (Wed, 08 Apr 2015).

Package 79/219HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Fletcher2013b 1.1.1
Mauro Castro
Snapshot Date: 2015-04-08 06:15:26 -0700 (Wed, 08 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_3_0/experiment/pkgs/Fletcher2013b
Last Changed Rev: 3075 / Revision: 3266
Last Changed Date: 2014-10-13 14:52:40 -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 

Summary

Package: Fletcher2013b
Version: 1.1.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Fletcher2013b_1.1.1.tar.gz
StartedAt: 2015-04-08 09:42:32 -0700 (Wed, 08 Apr 2015)
EndedAt: 2015-04-08 09:56:10 -0700 (Wed, 08 Apr 2015)
EllapsedTime: 818.6 seconds
RetCode: 0
Status:  OK 
CheckDir: Fletcher2013b.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Fletcher2013b_1.1.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.0-data-experiment/meat/Fletcher2013b.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Fletcher2013b/DESCRIPTION’ ... OK
* this is package ‘Fletcher2013b’ version ‘1.1.1’
* 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 ‘Fletcher2013b’ can be installed ... [37s/78s] OK
* checking installed package size ... NOTE
  installed size is 265.8Mb
  sub-directories of 1Mb or more:
    data  262.0Mb
    doc     3.6Mb
* 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
draw2venn: no visible global function definition for ‘gpar’
draw2venn: no visible global function definition for ‘textGrob’
draw2venn: no visible global function definition for ‘linesGrob’
Fletcher2013gsea.regulons: no visible global function definition for
  ‘tna.gsea1’
Fletcher2013pipeline.consensusnet: no visible global function
  definition for ‘tni.dpi.filter’
Fletcher2013pipeline.consensusnet: no visible global function
  definition for ‘graph.adjacency’
Fletcher2013pipeline.consensusnet: no visible global function
  definition for ‘get.edgelist’
Fletcher2013pipeline.consensusnet: no visible global function
  definition for ‘E’
Fletcher2013pipeline.consensusnet: no visible global function
  definition for ‘E<-’
Fletcher2013pipeline.consensusnet: no visible global function
  definition for ‘V’
Fletcher2013pipeline.consensusnet: no visible global function
  definition for ‘V<-’
Fletcher2013pipeline.enrichmap: no visible global function definition
  for ‘tni.get’
Fletcher2013pipeline.enrichmap: no visible global function definition
  for ‘graph.adjacency’
Fletcher2013pipeline.enrichmap: no visible global function definition
  for ‘V’
Fletcher2013pipeline.enrichmap: no visible global function definition
  for ‘V<-’
Fletcher2013pipeline.enrichmap: no visible global function definition
  for ‘E’
Fletcher2013pipeline.enrichmap: no visible global function definition
  for ‘E<-’
Fletcher2013pipeline.mra1st: no visible global function definition for
  ‘tni.dpi.filter’
Fletcher2013pipeline.mra2nd: no visible global function definition for
  ‘tni.dpi.filter’
Fletcher2013pipeline.mraNormals: no visible global function definition
  for ‘tni.dpi.filter’
Fletcher2013pipeline.mraTALL: no visible global function definition for
  ‘tni.dpi.filter’
getTSSmap: no visible global function definition for ‘listDatasets’
* 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 ... [24s/37s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
rtni.data 4.797   0.67   8.377
* 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 were 2 notes.
See
  ‘/Users/biocbuild/bbs-3.0-data-experiment/meat/Fletcher2013b.Rcheck/00check.log’
for details.

Fletcher2013b.Rcheck/00install.out:

* installing *source* package ‘Fletcher2013b’ ...
** 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 (Fletcher2013b)

Fletcher2013b.Rcheck/Fletcher2013b-Ex.timings:

nameusersystemelapsed
Fletcher2013b.gsea.regulons0.0000.0000.001
Fletcher2013b.pipelines0.0010.0000.001
miscellaneous1.1620.0321.678
rtni.data4.7970.6708.377
siRNA0.0100.0000.021