BioC 3.0: CHECK report for globaltest on moscato1

Package: globaltest

Version: 5.20.0

Command: rm -rf globaltest.buildbin-libdir globaltest.Rcheck && mkdir globaltest.buildbin-libdir globaltest.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=globaltest.buildbin-libdir globaltest_5.20.0.tar.gz >globaltest.Rcheck\00install.out 2>&1 && cp globaltest.Rcheck\00install.out globaltest-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=globaltest.buildbin-libdir --install="check:globaltest-install.out" --force-multiarch --no-vignettes --timings globaltest_5.20.0.tar.gz

StartedAt: 2015-04-10 01:44:32 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 01:47:33 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 180.6 seconds

RetCode: 0

Status:  OK

CheckDir: globaltest.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf globaltest.buildbin-libdir globaltest.Rcheck && mkdir globaltest.buildbin-libdir globaltest.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=globaltest.buildbin-libdir globaltest_5.20.0.tar.gz >globaltest.Rcheck\00install.out 2>&1 && cp globaltest.Rcheck\00install.out globaltest-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=globaltest.buildbin-libdir --install="check:globaltest-install.out" --force-multiarch --no-vignettes --timings globaltest_5.20.0.tar.gz
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* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/globaltest.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* 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 whether package 'globaltest' can be installed ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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:
  'Biobase' 'GO.db' 'GSEABase' 'KEGG.db' 'Rgraphviz' 'annotate'
  '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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [10s] OK
** running examples for arch 'x64' ... [11s] 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
  'D:/biocbld/bbs-3.0-bioc/meat/globaltest.Rcheck/00check.log'
for details.

install for i386

* 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

install for x64

* installing *source* package 'globaltest' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'globaltest' as globaltest_5.20.0.zip
* DONE (globaltest)

name	user	system	elapsed
comparative	2.17	0.00	2.17
diagnostics	0.81	0.00	0.81
genesettesting	0	0	0
goodnessoffit	0.81	0.00	0.81
gt	0.58	0.00	0.58
gt.object-class	0.37	0.00	0.42
gtoptions	0	0	0
mlogit	0.02	0.00	0.01
multtest	0.44	0.00	0.44

name	user	system	elapsed
comparative	1.72	0.00	1.71
diagnostics	0.98	0.02	1.00
genesettesting	0	0	0
goodnessoffit	0.86	0.00	0.86
gt	0.73	0.00	0.73
gt.object-class	0.42	0.01	0.44
gtoptions	0	0	0
mlogit	0	0	0
multtest	0.52	0.00	0.52