Back to the "Multiple platform build/check report"

BioC experimental data: CHECK report for Mulder2012 on petty

This page was generated on 2013-10-08 16:07:36 -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: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Mulder2012_0.2.3.tar.gz
StartedAt: 2013-10-08 14:13:24 -0700 (Tue, 08 Oct 2013)
EndedAt: 2013-10-08 14:20:14 -0700 (Tue, 08 Oct 2013)
EllapsedTime: 409.9 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: Mulder2012.Rcheck
Warnings: 1

Command output

* using log directory '/Users/biocbuild/bbs-2.12-data-experiment/meat/Mulder2012.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* 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 ... [22s/24s] WARNING
Found the following significant warnings:
  Warning: package 'KEGG.db' was built under R version 3.1.0
  Warning: package 'KEGG.db' was built under R version 3.1.0
See '/Users/biocbuild/bbs-2.12-data-experiment/meat/Mulder2012.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is 24.2Mb
  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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning.
NOTE: There were 2 notes.
See
  '/Users/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: package 'KEGG.db' was built under R version 3.1.0
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: package 'KEGG.db' was built under R version 3.1.0
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.BMfitting0.0050.0020.006
Arora2010.InferPAN0.0040.0020.006
Arora2010.ModuleSearchByPvclust0.0080.0020.009
Arora2010.fig0.2570.0020.259
Arora2010.hypergeo0.0040.0020.006
Arora2010.module.visualize0.0040.0010.006
Arora2010.pipeline0.0040.0020.005
GSEARandomWalkFig0.0040.0010.006
Mulder2012.BMfitting0.0040.0020.006
Mulder2012.InferPAN0.0040.0020.006
Mulder2012.ModuleSearchByPvclust0.0040.0020.006
Mulder2012.PPIPre0.0040.0010.005
Mulder2012.PPIenrich0.0060.0020.009
Mulder2012.RNAiPre0.0040.0020.005
Mulder2012.fig0.0040.0010.005
Mulder2012.module.visualize0.0040.0010.006
Mulder2012.pipeline0.0040.0010.005
data-Arora20101.5310.0461.578
data-Mulder20120.6460.0450.691