BioC 2.14: CHECK report for clusterProfiler on morelia

Package: clusterProfiler

Version: 1.12.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch clusterProfiler_1.12.0.tar.gz

StartedAt: 2014-10-07 22:02:50 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 22:05:07 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 137.0 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: clusterProfiler.Rcheck

Warnings: 1

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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 clusterProfiler_1.12.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/clusterProfiler.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘clusterProfiler/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘clusterProfiler’ 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 ‘clusterProfiler’ can be installed ... [11s/12s] 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 ... WARNING
Duplicated \argument entries in documentation object 'show':
  ‘object’
Objects in \usage without \alias in documentation object 'show':
  ‘\S4method{show}{compareClusterResult}’
  ‘\S4method{show}{groupGOResult}’

Objects in \usage without \alias in documentation object 'summary':
  ‘\S4method{summary}{compareClusterResult}’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... [15s/16s] 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

WARNING: There was 1 warning.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/clusterProfiler.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
compareCluster	4.706	0.147	4.883
enrichGO	0.001	0.000	0.000
enrichKEGG	0.515	0.015	0.529
groupGO	3.675	0.340	4.015