BioC 2.13: CHECK report for topGO on zin1

Package: topGO

Version: 2.14.0

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings topGO_2.14.0.tar.gz

StartedAt: 2014-04-05 04:23:11 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 04:25:20 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 129.4 seconds

RetCode: 0

Status:  OK

CheckDir: topGO.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/topGO.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (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 ‘2.14.0’
* 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 ... [10s/10s] 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 installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘topGO.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [23s/23s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
topGOdata-class 6.933  0.064   7.016
* 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
  ‘/home/biocbuild/bbs-2.13-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	0.204	0.000	0.207
annFUN	1.768	0.040	1.864
classicCount-class	0.012	0.000	0.011
classicExpr-class	0.008	0.000	0.007
classicScore-class	0.012	0.000	0.010
dagFunctions	0.004	0.000	0.006
diagnosticMethods	0.380	0.004	0.385
elimExpr-class	0.016	0.000	0.015
elimScore-class	0.012	0.000	0.016
geneList	0.016	0.008	0.025
getPvalues	3.848	0.072	3.929
getSigGroups	3.904	0.008	3.927
groupGOTerms	0.384	0.008	0.390
inducedGraph	0.048	0.004	0.053
parentChild-class	0.028	0.000	0.030
printGraph-methods	0.004	0.000	0.002
topGOdata-class	6.933	0.064	7.016
topGOresult-class	0.268	0.000	0.276