BioC 2.13: CHECK report for NCIgraph on zin1

Package: NCIgraph

Version: 1.10.0

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings NCIgraph_1.10.0.tar.gz

StartedAt: 2014-04-05 02:42:38 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 02:43:45 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 67.4 seconds

RetCode: 0

Status:  OK

CheckDir: NCIgraph.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/NCIgraph.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘NCIgraph/DESCRIPTION’ ... OK
* this is package ‘NCIgraph’ version ‘1.10.0’
* 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 ... [4s/4s] 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 installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘NCIgraph.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [26s/26s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
getSubtype.NCIgraph 7.801  0.000   7.823
getNCIPathways      7.588  0.024   7.624
translateNCI2GeneID 7.512  0.004   7.532
* 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 3 notes.
See
  ‘/home/biocbuild/bbs-2.13-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	0.392	0.016	0.408
getNCIPathways	7.588	0.024	7.624
getSubtype.NCIgraph	7.801	0.000	7.823
parseNCInetwork	0.344	0.000	0.343
translateNCI2GeneID	7.512	0.004	7.532