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BioC experimental data: CHECK report for Mulder2012 on george2

This page was generated on 2013-10-08 16:07:19 -0700 (Tue, 08 Oct 2013).

Package 106/156HostnameOS / ArchBUILDCHECKBUILD BIN
Mulder2012 0.2.3
Xin Wang
Snapshot Date: 2013-10-08 10:15:19 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/Mulder2012
Last Changed Rev: 2317 / Revision: 2510
Last Changed Date: 2013-04-03 15:11:40 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK [ OK ]
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: Mulder2012
Version: 0.2.3
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings Mulder2012_0.2.3.tar.gz
StartedAt: 2013-10-08 13:04:24 -0700 (Tue, 08 Oct 2013)
EndedAt: 2013-10-08 13:10:35 -0700 (Tue, 08 Oct 2013)
EllapsedTime: 370.8 seconds
RetCode: 0
Status:  OK 
CheckDir: Mulder2012.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.12-data-experiment/meat/Mulder2012.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 ‘Mulder2012/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Mulder2012’ version ‘0.2.3’
* 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 ‘Mulder2012’ can be installed ... [35s/41s] OK
* checking installed package size ... NOTE
  installed size is 24.3Mb
  sub-directories of 1Mb or more:
    data  19.9Mb
    doc    4.2Mb
* 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 ... NOTE
Arora2010.fig: no visible binding for global variable ‘bm_Arora2010’
Arora2010.fig: no visible binding for global variable ‘pan_Arora2010’
Arora2010.pipeline: no visible binding for global variable ‘Arora2010’
Mulder2012.PPIPre: no visible binding for global variable
  ‘PINdbProteins’
Mulder2012.PPIPre : <anonymous>: no visible binding for global variable
  ‘PINdbProteins’
Mulder2012.fig: no visible binding for global variable ‘bm_Mulder2012’
Mulder2012.fig: no visible binding for global variable ‘Mulder2012’
Mulder2012.fig: no visible binding for global variable ‘PPI’
Mulder2012.fig: no visible binding for global variable
  ‘bm_ext_Mulder2012’
Mulder2012.fig: no visible binding for global variable
  ‘pan_ext_Mulder2012’
* 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 examples ... [21s/22s] 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-2.12-data-experiment/meat/Mulder2012.Rcheck/00check.log’
for details.

Mulder2012.Rcheck/00install.out:

* installing *source* package ‘Mulder2012’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning in .simpleDuplicateClass(def, prev) :
  the specification for class “numeric_Or_integer” in package ‘PANR’ seems equivalent to one from package ‘HTSanalyzeR’ and is not turning on duplicate class definitions for this class
Warning in .simpleDuplicateClass(def, prev) :
  the specification for S3 class “AsIs” in package ‘XMLRPC’ seems equivalent to one from package ‘BiocGenerics’ and is 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
Warning in .simpleDuplicateClass(def, prev) :
  the specification for class “numeric_Or_integer” in package ‘PANR’ seems equivalent to one from package ‘HTSanalyzeR’ and is not turning on duplicate class definitions for this class
Warning in .simpleDuplicateClass(def, prev) :
  the specification for S3 class “AsIs” in package ‘XMLRPC’ seems equivalent to one from package ‘BiocGenerics’ and is not turning on duplicate class definitions for this class
* DONE (Mulder2012)

Mulder2012.Rcheck/Mulder2012-Ex.timings:

nameusersystemelapsed
Arora2010.BMfitting0.6240.0080.657
Arora2010.InferPAN0.0240.0040.024
Arora2010.ModuleSearchByPvclust0.0170.0000.016
Arora2010.fig0.0160.0000.016
Arora2010.hypergeo0.0160.0000.019
Arora2010.module.visualize0.0120.0000.015
Arora2010.pipeline0.0240.0000.024
GSEARandomWalkFig0.0280.0000.025
Mulder2012.BMfitting0.0240.0000.024
Mulder2012.InferPAN0.0240.0000.025
Mulder2012.ModuleSearchByPvclust0.0160.0000.017
Mulder2012.PPIPre0.0160.0000.015
Mulder2012.PPIenrich0.0240.0040.027
Mulder2012.RNAiPre0.0160.0000.014
Mulder2012.fig0.0120.0000.015
Mulder2012.module.visualize0.0280.0000.026
Mulder2012.pipeline0.0240.0000.024
data-Arora20102.5280.0523.237
data-Mulder20120.5640.0440.627