BioC 3.0: CHECK report for clipper on oaxaca

Package: clipper

Version: 1.6.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch clipper_1.6.2.tar.gz

StartedAt: 2015-04-09 22:22:06 -0700 (Thu, 09 Apr 2015)

EndedAt: 2015-04-09 22:28:42 -0700 (Thu, 09 Apr 2015)

EllapsedTime: 395.7 seconds

RetCode: 0

Status:  OK

CheckDir: clipper.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 clipper_1.6.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/clipper.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 ‘clipper/DESCRIPTION’ ... OK
* this is package ‘clipper’ version ‘1.6.2’
* 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 ‘clipper’ can be installed ... [32s/32s] 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 dependencies in R code ... NOTE
'library' or 'require' call to ‘RCytoscape’ in package code.
  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
plotInCytoscape: no visible global function definition for
  ‘initEdgeAttribute’
plotInCytoscape: no visible global function definition for
  ‘CytoscapeConnection’
plotInCytoscape: no visible global function definition for
  ‘getWindowList’
plotInCytoscape: no visible global function definition for
  ‘deleteWindow’
plotInCytoscape: no visible global function definition for
  ‘new.CytoscapeWindow’
plotInCytoscape: no visible global function definition for
  ‘deleteNodeAttribute’
plotInCytoscape: no visible global function definition for
  ‘displayGraph’
plotInCytoscape: no visible global function definition for
  ‘setNodeColorDirect’
plotInCytoscape: no visible global function definition for
  ‘layoutNetwork’
plotInCytoscape: no visible global function definition for ‘redraw’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... NOTE
The following files should probably not be installed:
  ‘Cytoscape.png’

Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
* checking files in ‘vignettes’ ... OK
* checking examples ... [67s/67s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
clipperAllRoots 12.713  0.225  13.143
pathwayTest      9.841  0.099   9.974
clipper          7.835  0.173   8.142
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [22s/22s]
 [22s/22s] OK
* 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 3 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/clipper.Rcheck/00check.log’
for details.

* installing *source* package ‘clipper’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (clipper)

name	user	system	elapsed
clipper	7.835	0.173	8.142
clipperAllRoots	12.713	0.225	13.143
cliqueMeanTest	3.462	0.051	3.525
cliqueMixedTest	3.888	0.072	4.145
cliquePairedTest	3.994	0.076	4.081
cliqueVarianceTest	3.364	0.070	3.445
deleteEdge	0.247	0.001	0.249
easyClip	3.235	0.050	3.300
getGraphEntryGenes	0.306	0.003	0.309
getJunctionTreePaths	0.345	0.002	0.348
nameCliques	0.002	0.000	0.001
pathwayTest	9.841	0.099	9.974
plotInCytoscape	0.001	0.000	0.001
prunePaths	0.005	0.001	0.004