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BioC experimental data: CHECK report for Mulder2012 on zin1

This page was generated on 2014-04-04 17:28:52 -0700 (Fri, 04 Apr 2014).

Package 124/181HostnameOS / ArchBUILDCHECKBUILD BIN
Mulder2012 0.2.5
Xin Wang
Snapshot Date: 2014-04-04 06:15:32 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_2_13/experiment/pkgs/Mulder2012
Last Changed Rev: 2557 / Revision: 2768
Last Changed Date: 2013-11-01 13:36:05 -0700 (Fri, 01 Nov 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: Mulder2012
Version: 0.2.5
Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings Mulder2012_0.2.5.tar.gz
StartedAt: 2014-04-04 09:33:07 -0700 (Fri, 04 Apr 2014)
EndedAt: 2014-04-04 09:36:58 -0700 (Fri, 04 Apr 2014)
EllapsedTime: 231.2 seconds
RetCode: 0
Status:  OK 
CheckDir: Mulder2012.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.13-data-experiment/meat/Mulder2012.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 ‘Mulder2012/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Mulder2012’ version ‘0.2.5’
* 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 ... [23s/24s] OK
* checking installed package size ... NOTE
  installed size is 22.5Mb
  sub-directories of 1Mb or more:
    data  19.9Mb
    doc    2.4Mb
* 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 ... NOTE
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘KEGG.db’ ‘org.Hs.eg.db’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 files in ‘vignettes’ ... OK
* checking examples ... [13s/13s] 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

NOTE: There were 3 notes.
See
  ‘/home/biocbuild/bbs-2.13-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
Note: the specification for class “numeric_Or_integer” in package ‘PANR’ seems equivalent to one from package ‘HTSanalyzeR’: not turning on duplicate class definitions for this class.
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 class “numeric_Or_integer” in package ‘PANR’ seems equivalent to one from package ‘HTSanalyzeR’: not turning on duplicate class definitions for this class.
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 (Mulder2012)

Mulder2012.Rcheck/Mulder2012-Ex.timings:

nameusersystemelapsed
Arora2010.BMfitting0.2640.0000.266
Arora2010.InferPAN0.0000.0040.005
Arora2010.ModuleSearchByPvclust0.0000.0000.004
Arora2010.fig0.0000.0000.003
Arora2010.hypergeo0.0040.0000.000
Arora2010.module.visualize0.0040.0000.006
Arora2010.pipeline0.0040.0000.003
GSEARandomWalkFig0.0000.0040.004
Mulder2012.BMfitting0.0040.0000.003
Mulder2012.InferPAN0.0040.0000.003
Mulder2012.ModuleSearchByPvclust0.0040.0000.003
Mulder2012.PPIPre0.0000.0040.006
Mulder2012.PPIenrich0.0040.0000.006
Mulder2012.RNAiPre0.0040.0000.005
Mulder2012.fig0.0040.0000.005
Mulder2012.module.visualize0.0000.0080.006
Mulder2012.pipeline0.0040.0040.004
data-Arora20101.1640.0241.192
data-Mulder20120.7920.0040.798