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BioC 2.13: CHECK report for globaltest on perceval

This page was generated on 2014-04-05 09:51:42 -0700 (Sat, 05 Apr 2014).

Package 313/750HostnameOS / ArchBUILDCHECKBUILD BIN
globaltest 5.16.0
Jelle Goeman
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/globaltest
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 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: globaltest
Version: 5.16.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch globaltest_5.16.0.tar.gz
StartedAt: 2014-04-05 01:41:44 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 01:44:34 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 169.9 seconds
RetCode: 0
Status:  OK 
CheckDir: globaltest.Rcheck
Warnings: 0

Command output

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/globaltest.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘globaltest/DESCRIPTION’ ... OK
* this is package ‘globaltest’ version ‘5.16.0’
* 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 ‘globaltest’ can be installed ... [14s/14s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘annotate’ ‘Biobase’ ‘survival’
A package should be listed in only one of these fields.
* 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: ‘multtest’
  All declared Imports should be used.
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
p.adjust,gt.object: warning in grep(method, p.adjust.methods, ign = T):
  partial argument match of 'ign' to 'ignore.case'
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘GlobalTest.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [14s/14s] 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 4 notes.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/globaltest.Rcheck/00check.log’
for details.

globaltest.Rcheck/00install.out:

* installing *source* package ‘globaltest’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘sort’ from package ‘base’ in package ‘globaltest’
Creating a generic function for ‘model.matrix’ from package ‘stats’ in package ‘globaltest’
Creating a generic function for ‘coefficients’ from package ‘stats’ in package ‘globaltest’
Creating a generic function for ‘fitted.values’ from package ‘stats’ in package ‘globaltest’
Creating a generic function for ‘residuals’ from package ‘stats’ in package ‘globaltest’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (globaltest)

globaltest.Rcheck/globaltest-Ex.timings:

nameusersystemelapsed
comparative1.6540.0251.698
diagnostics0.7240.0170.755
genesettesting0.0070.0010.009
goodnessoffit1.3740.0341.457
gt1.4070.0241.440
gt.object-class1.0100.0291.052
gtoptions0.0060.0060.012
mlogit0.0230.0070.029
multtest0.4110.0340.446