BioC experimental data: CHECK report for Mulder2012 on petty

* 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.

* 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)

name	user	system	elapsed
Arora2010.BMfitting	0.005	0.002	0.006
Arora2010.InferPAN	0.004	0.002	0.006
Arora2010.ModuleSearchByPvclust	0.008	0.002	0.009
Arora2010.fig	0.257	0.002	0.259
Arora2010.hypergeo	0.004	0.002	0.006
Arora2010.module.visualize	0.004	0.001	0.006
Arora2010.pipeline	0.004	0.002	0.005
GSEARandomWalkFig	0.004	0.001	0.006
Mulder2012.BMfitting	0.004	0.002	0.006
Mulder2012.InferPAN	0.004	0.002	0.006
Mulder2012.ModuleSearchByPvclust	0.004	0.002	0.006
Mulder2012.PPIPre	0.004	0.001	0.005
Mulder2012.PPIenrich	0.006	0.002	0.009
Mulder2012.RNAiPre	0.004	0.002	0.005
Mulder2012.fig	0.004	0.001	0.005
Mulder2012.module.visualize	0.004	0.001	0.006
Mulder2012.pipeline	0.004	0.001	0.005
data-Arora2010	1.531	0.046	1.578
data-Mulder2012	0.646	0.045	0.691

BioC experimental data: CHECK report for Mulder2012 on petty

Summary

Command output