BioC 3.2: CHECK report for clusterProfiler on zin1

Package: clusterProfiler

Version: 2.3.6

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings clusterProfiler_2.3.6.tar.gz

StartedAt: 2015-08-23 22:39:29 -0700 (Sun, 23 Aug 2015)

EndedAt: 2015-08-23 22:41:37 -0700 (Sun, 23 Aug 2015)

EllapsedTime: 127.8 seconds

RetCode: 1

Status:  ERROR

CheckDir: clusterProfiler.Rcheck

Warnings: NA

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings clusterProfiler_2.3.6.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/clusterProfiler.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (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 ‘2.3.6’
* 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 ... NOTE
Found the following hidden files and directories:
  .svnignore
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘clusterProfiler’ can be installed ... [10s/10s] 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 ... NOTE
plot,compareClusterResult-ANY : .local: no visible global function
  definition for ‘barplot.enrichResult’
* 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘clusterProfiler-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: compareCluster
> ### Title: Compare gene clusters functional profile
> ### Aliases: compareCluster
> ### Keywords: manip
> 
> ### ** Examples
> 
> data(gcSample)
> xx <- compareCluster(gcSample, fun="enrichKEGG",
+                      organism="human", pvalueCutoff=0.05)
Error in compareCluster(gcSample, fun = "enrichKEGG", organism = "human",  : 
  No enrichment found in any of gene cluster, please check your input...
Execution halted
* 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

Status: 1 ERROR, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/clusterProfiler.Rcheck/00check.log’
for details.

* installing *source* package ‘clusterProfiler’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import by ‘graph::.__C__dist’ when loading ‘topGO’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import by ‘graph::.__C__dist’ when loading ‘topGO’
* DONE (clusterProfiler)

name	user	system	elapsed