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BioC 3.0: CHECK report for graphite on zin1

This page was generated on 2015-04-10 09:39:32 -0700 (Fri, 10 Apr 2015).

Package 402/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
graphite 1.12.0
Gabriele Sales
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/graphite
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  OK  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: graphite
Version: 1.12.0
Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings graphite_1.12.0.tar.gz
StartedAt: 2015-04-10 00:49:05 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 00:53:54 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 289.0 seconds
RetCode: 0
Status:  OK 
CheckDir: graphite.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings graphite_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/graphite.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘graphite/DESCRIPTION’ ... OK
* this is package ‘graphite’ version ‘1.12.0’
* 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 ‘graphite’ can be installed ... [20s/20s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 dependencies in R code ... NOTE
'library' or 'require' calls in package code:
  ‘DEGraph’ ‘RCytoscape’ ‘SPIA’ ‘clipper’ ‘topologyGSA’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
cytoscapePlot: no visible global function definition for
  ‘initEdgeAttribute’
cytoscapePlot: no visible global function definition for
  ‘CytoscapeConnection’
cytoscapePlot: no visible global function definition for
  ‘getWindowList’
cytoscapePlot: no visible global function definition for ‘deleteWindow’
cytoscapePlot: no visible global function definition for
  ‘new.CytoscapeWindow’
cytoscapePlot: no visible global function definition for ‘displayGraph’
cytoscapePlot: no visible global function definition for
  ‘setEdgeTargetArrowRule’
cytoscapePlot: no visible global function definition for
  ‘layoutNetwork’
cytoscapePlot: no visible global function definition for ‘redraw’
runClipperSingle: no visible global function definition for ‘easyClip’
runDEGraphSingle: no visible global function definition for
  ‘testOneGraph’
switchTest: no visible binding for global variable ‘pathway.var.test’
switchTest: no visible binding for global variable ‘pathway.mean.test’
* 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 ... NOTE
  Note: found 28 marked UTF-8 strings
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [151s/165s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
runClipperMulti 113.915  0.152 114.836
runClipper       21.069  0.380  26.943
runSPIA           5.573  0.072   7.435
runDEGraph        1.524  0.096   5.854
* 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 4 notes.
See
  ‘/home/biocbuild/bbs-3.0-bioc/meat/graphite.Rcheck/00check.log’
for details.

graphite.Rcheck/00install.out:

* installing *source* package ‘graphite’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (graphite)

graphite.Rcheck/graphite-Ex.timings:

nameusersystemelapsed
convertIdentifiers1.0440.0801.364
cytoscapePlot0.0040.0000.001
pathwayGraph0.0160.0000.018
runClipper21.069 0.38026.943
runClipperMulti113.915 0.152114.836
runDEGraph1.5240.0965.854
runDEGraphMulti0.5000.0080.511
runSPIA5.5730.0727.435
runTopologyGSA1.4640.0121.919
runTopologyGSAMulti0.4920.0080.502