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BioC 3.0: CHECK report for clipper on zin1

This page was generated on 2015-04-10 09:40:31 -0700 (Fri, 10 Apr 2015).

Package 162/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
clipper 1.6.2
Paolo Martini
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/clipper
Last Changed Rev: 97277 / Revision: 102249
Last Changed Date: 2014-12-02 07:35:04 -0800 (Tue, 02 Dec 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: clipper
Version: 1.6.2
Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings clipper_1.6.2.tar.gz
StartedAt: 2015-04-09 22:39:25 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 22:44:54 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 329.1 seconds
RetCode: 0
Status:  OK 
CheckDir: clipper.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings clipper_1.6.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/clipper.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 ‘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 ... [28s/28s] 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 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 ... [57s/58s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
clipperAllRoots 11.248  0.080  11.349
pathwayTest      8.793  0.028   8.832
clipper          6.429  0.100   6.548
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [19s/19s]
 [19s/19s] 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
  ‘/home/biocbuild/bbs-3.0-bioc/meat/clipper.Rcheck/00check.log’
for details.

clipper.Rcheck/00install.out:

* 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)

clipper.Rcheck/clipper-Ex.timings:

nameusersystemelapsed
clipper6.4290.1006.548
clipperAllRoots11.248 0.08011.349
cliqueMeanTest3.2170.0403.262
cliqueMixedTest3.1800.0283.277
cliquePairedTest3.4280.0323.464
cliqueVarianceTest3.1960.0203.224
deleteEdge0.2000.0040.202
easyClip2.9280.0323.010
getGraphEntryGenes0.2520.0000.254
getJunctionTreePaths0.2760.0000.278
nameCliques0.0000.0000.001
pathwayTest8.7930.0288.832
plotInCytoscape000
prunePaths0.0040.0000.003