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BioC 2.12: CHECK report for clusterProfiler on george2

This page was generated on 2013-10-09 09:37:42 -0700 (Wed, 09 Oct 2013).

Package 130/671HostnameOS / ArchBUILDCHECKBUILD BIN
clusterProfiler 1.8.0
Guangchuang Yu
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/clusterProfiler
Last Changed Rev: 75263 / Revision: 81334
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK [ WARNINGS ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  WARNINGS  OK 

Summary

Package: clusterProfiler
Version: 1.8.0
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings clusterProfiler_1.8.0.tar.gz
StartedAt: 2013-10-09 01:01:17 -0700 (Wed, 09 Oct 2013)
EndedAt: 2013-10-09 01:04:54 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 217.4 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: clusterProfiler.Rcheck
Warnings: 1

Command output

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/clusterProfiler.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-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 ‘1.8.0’
* 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 ... [18s/18s] OK
* checking installed package size ... OK
* checking package 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 for unstated 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 ... WARNING
Codoc mismatches from documentation object 'Gff2GeneTable':
Gff2GeneTable
  Code: function(gffFile, compress = TRUE)
  Docs: function(gffFile)
  Argument names in code not in docs:
    compress

* 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 examples ... [24s/28s] OK
Examples with CPU or elapsed time > 5s
          user system elapsed
groupGO 11.217  0.412  13.278
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning.
See
  ‘/home/biocbuild/bbs-2.12-bioc/meat/clusterProfiler.Rcheck/00check.log’
for details.

clusterProfiler.Rcheck/00install.out:

* 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)

clusterProfiler.Rcheck/clusterProfiler-Ex.timings:

nameusersystemelapsed
compareCluster2.6880.0682.877
enrichGO0.0200.0040.022
enrichKEGG0.4000.0160.430
groupGO11.217 0.41213.278