globaltest 5.20.0
Jelle Goeman
| Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/globaltest | | Last Changed Rev: 95439 / Revision: 102249 | | Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | OK | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | [ OK ] | OK |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch globaltest_5.20.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/globaltest.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 ‘globaltest/DESCRIPTION’ ... OK
* this is package ‘globaltest’ version ‘5.20.0’
* 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 ... [16s/19s] 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
'library' or 'require' calls in package code:
‘annotate’ ‘Biobase’ ‘GO.db’ ‘GSEABase’ ‘KEGG.db’ ‘Rgraphviz’
‘survival’
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespace in Imports field not imported from: ‘multtest’
All declared Imports should be used.
* 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'
draw: no visible global function definition for ‘buildNodeList’
draw: no visible global function definition for ‘buildEdgeList’
draw: no visible binding for global variable ‘name’
draw: no visible binding for global variable ‘from’
draw: no visible binding for global variable ‘to’
draw: no visible global function definition for ‘agopen’
draw: no visible global function definition for ‘getNodeXY’
gtBroad: no visible binding for global variable ‘collectionType’
gtBroad: no visible binding for global variable ‘bcCategory’
gtBroad: no visible global function definition for ‘mapIdentifiers’
gtBroad: no visible global function definition for
‘AnnotationIdentifier’
gtBroad: no visible binding for global variable ‘geneIds’
gtGO: no visible global function definition for ‘mappedkeys’
gtGO: no visible binding for global variable ‘Ontology’
gtGO : <anonymous>: no visible global function definition for ‘keys’
gtKEGG: no visible global function definition for ‘mappedkeys’
* 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 files in ‘vignettes’ ... OK
* checking examples ... [15s/15s] 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
NOTE: There were 3 notes.
See
‘/Users/biocbuild/bbs-3.0-bioc/meat/globaltest.Rcheck/00check.log’
for details.
* 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)