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BioC experimental data: CHECK report for pumadata on perceval

This page was generated on 2015-04-08 17:41:23 -0700 (Wed, 08 Apr 2015).

Package 173/219HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pumadata 2.1.1
Richard Pearson
Snapshot Date: 2015-04-08 06:15:26 -0700 (Wed, 08 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_3_0/experiment/pkgs/pumadata
Last Changed Rev: 3075 / Revision: 3266
Last Changed Date: 2014-10-13 14:52:40 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  WARNINGS 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  WARNINGS  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ WARNINGS ] OK 

Summary

Package: pumadata
Version: 2.1.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch pumadata_2.1.1.tar.gz
StartedAt: 2015-04-08 10:28:30 -0700 (Wed, 08 Apr 2015)
EndedAt: 2015-04-08 10:32:42 -0700 (Wed, 08 Apr 2015)
EllapsedTime: 252.1 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: pumadata.Rcheck
Warnings: 1

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch pumadata_2.1.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.0-data-experiment/meat/pumadata.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pumadata/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pumadata’ version ‘2.1.1’
* 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 ‘pumadata’ can be installed ... [25s/28s] OK
* checking installed package size ... NOTE
  installed size is 100.6Mb
  sub-directories of 1Mb or more:
    data  100.5Mb
* 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 ... WARNING
Invalid citation information in ‘inst/CITATION’:
  Error in utils::readCitationFile(cfile, meta): attempt to set an attribute on NULL
* 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
'library' or 'require' call to ‘Biobase’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘affy’ ‘Biobase’ ‘oligo’ ‘puma’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File ‘pumadata/R/zzz.R’:
  .onLoad calls:
    require(Biobase)

Package startup functions should not change the search path.
See section ‘Good practice’ in '?.onAttach'.

.onLoad: no visible global function definition for ‘addVigs2WinMenu’
* 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 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
* DONE

WARNING: There was 1 warning.
NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-3.0-data-experiment/meat/pumadata.Rcheck/00check.log’
for details.

pumadata.Rcheck/00install.out:

* installing *source* package ‘pumadata’ ...
** 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 (pumadata)

pumadata.Rcheck/pumadata-Ex.timings:

nameusersystemelapsed
eset_estrogen_comb0.1270.0170.144
eset_estrogen_mmgmos0.5150.0140.539
eset_estrogen_pmmmgmos0.1370.0090.150
eset_estrogen_rma0.0330.0020.035
pumapca_estrogen0.3970.0030.401