BioC 2.14: CHECK report for topGO on petty

Package: topGO

Version: 2.16.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch topGO_2.16.0.tar.gz

StartedAt: 2014-10-08 00:27:28 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 00:32:16 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 287.5 seconds

RetCode: 0

Status:  OK

CheckDir: topGO.Rcheck

Warnings: 0

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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 topGO_2.16.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/topGO.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘topGO/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘topGO’ version ‘2.16.0’
* 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 ‘topGO’ can be installed ... [22s/23s] 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:
  ‘methods’ ‘graph’ ‘Biobase’ ‘SparseM’ ‘AnnotationDbi’
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' call to ‘GO.db’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘GO.db’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' call which should be '::': ‘globaltest:::p.value’
  See the note in ?`:::` about the use of this operator.
Missing object imported by a ':::' call: ‘globaltest:::globaltest’
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
getPvalues: warning in pt(t.stats, df = length(classlabel) - 2, lower =
  FALSE): partial argument match of 'lower' to 'lower.tail'
GOSumTest,classicScore: no visible binding for global variable
  ‘.PERMSUM.MAT’
GOSumTest,classicScore: no visible binding for global variable
  ‘.PERMSUM.LOOKUP’
* 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 ... [47s/48s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
topGOdata-class 14.298  0.247  14.651
getSigGroups     9.607  0.062   9.774
getPvalues       5.820  0.234   6.134
* 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 3 notes.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/topGO.Rcheck/00check.log’
for details.

* installing *source* package ‘topGO’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘print’ from package ‘base’ in package ‘topGO’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
* DONE (topGO)

name	user	system	elapsed
GOdata	0.080	0.005	0.084
annFUN	3.779	0.253	4.750
classicCount-class	0.001	0.000	0.001
classicExpr-class	0.004	0.000	0.005
classicScore-class	0.008	0.001	0.008
dagFunctions	0.001	0.000	0.001
diagnosticMethods	0.705	0.016	0.731
elimExpr-class	0.003	0.001	0.004
elimScore-class	0.001	0.001	0.002
geneList	0.007	0.001	0.008
getPvalues	5.820	0.234	6.134
getSigGroups	9.607	0.062	9.774
groupGOTerms	0.751	0.024	0.777
inducedGraph	0.099	0.003	0.101
parentChild-class	0.004	0.001	0.005
printGraph-methods	0.002	0.000	0.002
topGOdata-class	14.298	0.247	14.651
topGOresult-class	0.242	0.003	0.245