BioC 2.14: CHECK report for NCIgraph on petty

Package: NCIgraph

Version: 1.12.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch NCIgraph_1.12.0.tar.gz

StartedAt: 2014-10-07 23:11:48 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 23:14:23 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 154.9 seconds

RetCode: 0

Status:  OK

CheckDir: NCIgraph.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 NCIgraph_1.12.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/NCIgraph.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘NCIgraph/DESCRIPTION’ ... OK
* this is package ‘NCIgraph’ 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 ‘NCIgraph’ can be installed ... [8s/17s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘graph’
A package should be listed in only one of these fields.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getNCIPathways: warning in existing.CytoscapeWindow(w, copy.graph =
  TRUE): partial argument match of 'copy.graph' to
  'copy.graph.from.cytoscape.to.R'
* 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 ... [38s/53s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
translateNCI2GeneID 11.052  0.037  20.843
getNCIPathways      10.796  0.037  10.889
getSubtype.NCIgraph 10.770  0.035  15.539
* 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

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/NCIgraph.Rcheck/00check.log’
for details.

* installing *source* package ‘NCIgraph’ ...
** R
** data
** inst
** preparing package for lazy loading
Note: the specification for S3 class “AsIs” in package ‘XMLRPC’ seems equivalent to one from package ‘BiocGenerics’: not turning on duplicate class definitions for this class.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Note: the specification for S3 class “AsIs” in package ‘XMLRPC’ seems equivalent to one from package ‘BiocGenerics’: not turning on duplicate class definitions for this class.
* DONE (NCIgraph)

name	user	system	elapsed
NCI.demo.cyList	0.941	0.021	0.964
getNCIPathways	10.796	0.037	10.889
getSubtype.NCIgraph	10.770	0.035	15.539
parseNCInetwork	0.581	0.003	1.144
translateNCI2GeneID	11.052	0.037	20.843