BioC 3.0: CHECK report for graphite on oaxaca

Package: graphite

Version: 1.12.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch graphite_1.12.0.tar.gz

StartedAt: 2015-04-10 00:18:40 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 00:24:24 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 344.5 seconds

RetCode: 0

Status:  OK

CheckDir: graphite.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch graphite_1.12.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/graphite.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 ‘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 ... [24s/24s] 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [176s/182s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
runClipperMulti 132.582  1.612 136.674
runClipper       22.699  0.456  24.542
runSPIA           6.746  0.176   7.390
* 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
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/graphite.Rcheck/00check.log’
for details.

* 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)

name	user	system	elapsed
convertIdentifiers	1.351	0.094	1.479
cytoscapePlot	0.000	0.000	0.001
pathwayGraph	0.023	0.001	0.024
runClipper	22.699	0.456	24.542
runClipperMulti	132.582	1.612	136.674
runDEGraph	1.728	0.093	2.755
runDEGraphMulti	0.624	0.015	0.643
runSPIA	6.746	0.176	7.390
runTopologyGSA	1.851	0.017	1.950
runTopologyGSAMulti	0.616	0.006	0.627