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BioC 2.14: CHECK report for NCIgraph on petty

This page was generated on 2014-10-08 08:59:31 -0700 (Wed, 08 Oct 2014).

Package 528/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NCIgraph 1.12.0
Laurent Jacob
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/NCIgraph
Last Changed Rev: 88838 / Revision: 95116
Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ OK ] OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

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

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /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.

NCIgraph.Rcheck/00install.out:

* 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)

NCIgraph.Rcheck/NCIgraph-Ex.timings:

nameusersystemelapsed
NCI.demo.cyList0.9410.0210.964
getNCIPathways10.796 0.03710.889
getSubtype.NCIgraph10.770 0.03515.539
parseNCInetwork0.5810.0031.144
translateNCI2GeneID11.052 0.03720.843