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BioC 3.2: CHECK report for topGO on perceval

This page was generated on 2015-11-10 14:45:46 -0800 (Tue, 10 Nov 2015).

Package 1058/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
topGO 2.22.0
Adrian Alexa
Snapshot Date: 2015-11-09 16:24:09 -0800 (Mon, 09 Nov 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/topGO
Last Changed Rev: 109589 / Revision: 110496
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: topGO
Version: 2.22.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings topGO_2.22.0.tar.gz
StartedAt: 2015-11-10 10:15:41 -0800 (Tue, 10 Nov 2015)
EndedAt: 2015-11-10 10:18:10 -0800 (Tue, 10 Nov 2015)
EllapsedTime: 148.9 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: topGO.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings topGO_2.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/topGO.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* 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 ‘2.22.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘BiocGenerics’ ‘graph’ ‘Biobase’ ‘GO.db’ ‘AnnotationDbi’ ‘SparseM’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ... [12s/12s] WARNING
Found the following significant warnings:
  Warning: replacing previous import by ‘graph::.__C__dist’ when loading ‘topGO’
See ‘/Users/biocbuild/bbs-3.2-bioc/meat/topGO.Rcheck/00install.out’ for details.
* 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.
'library' or 'require' calls in package code:
  ‘multtest’ ‘Rgraphviz’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
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’
* 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'
GenTable,topGOdata : .local: warning in rank(-l[, ranksOf], ties =
  "first"): partial argument match of 'ties' to 'ties.method'
GenTable,topGOdata : .local: warning in rank(l[, ranksOf], ties =
  "first"): partial argument match of 'ties' to 'ties.method'
printGenes,topGOdata-character-missing : .local: warning in
  format.pval(pval[affID], dig = 3, eps = 1e-30): partial argument
  match of 'dig' to 'digits'
.getTermsDefinition: no visible global function definition for
  ‘dbGetQuery’
.getTermsDefinition: no visible global function definition for
  ‘GO_dbconn’
annFUN.db: no visible global function definition for ‘dbGetQuery’
annFUN.org: no visible global function definition for ‘dbGetQuery’
getPvalues: no visible global function definition for ‘mt.teststat’
getPvalues: no visible global function definition for ‘mt.rawp2adjp’
GOplot: no visible global function definition for ‘getDefaultAttrs’
GOplot: no visible global function definition for ‘agopen’
GOplot.counts : plotSigChart : buildDrawing : <anonymous>: no visible
  global function definition for ‘getNodeCenter’
GOplot.counts : plotSigChart : buildDrawing : <anonymous>: no visible
  global function definition for ‘pieGlyph’
GOplot.counts : plotSigChart : buildDrawing : <anonymous>: no visible
  global function definition for ‘getX’
GOplot.counts : plotSigChart : buildDrawing : <anonymous>: no visible
  global function definition for ‘getY’
GOplot.counts : plotSigChart : buildDrawing : <anonymous>: no visible
  global function definition for ‘getNodeLW’
GOplot.counts : plotSigChart : buildDrawing : <anonymous>: no visible
  global function definition for ‘drawTxtLabel’
GOplot.counts : plotSigChart : buildDrawing : <anonymous>: no visible
  global function definition for ‘txtLabel’
GOplot.counts : plotSigChart: no visible global function definition for
  ‘AgNode’
GOplot.counts : plotSigChart : <anonymous>: no visible global function
  definition for ‘name’
GOplot.counts : plotSigChart : <anonymous>: no visible global function
  definition for ‘getNodeCenter’
GOplot.counts : plotSigChart: no visible global function definition for
  ‘getNodeXY’
GOplot.counts : plotSigChart: no visible global function definition for
  ‘getY’
GOplot.counts: no visible global function definition for
  ‘getDefaultAttrs’
GOplot.counts: no visible global function definition for ‘agopen’
groupGOTerms: no visible global function definition for ‘dbGetQuery’
groupGOTerms: no visible global function definition for ‘GO_dbconn’
printDOT: no visible global function definition for ‘getDefaultAttrs’
printDOT: no visible global function definition for ‘toDot’
GOSumTest,classicScore: no visible binding for global variable
  ‘.PERMSUM.MAT’
GOSumTest,classicScore: no visible binding for global variable
  ‘.PERMSUM.LOOKUP’
initialize,classicExpr : .local: no visible global function definition
  for ‘error’
scoresInTerm,topGOdata-missing : .local: no visible global function
  definition for ‘scoreInNode’
* 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 ... [25s/25s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
topGOdata-class 7.996  0.146    8.18
* 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

Status: 1 WARNING, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/topGO.Rcheck/00check.log’
for details.


topGO.Rcheck/00install.out:

* installing *source* package ‘topGO’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import by ‘graph::.__C__dist’ when loading ‘topGO’
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
Warning: replacing previous import by ‘graph::.__C__dist’ when loading ‘topGO’

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

topGO.Rcheck/topGO-Ex.timings:

nameusersystemelapsed
GOdata0.0490.0030.051
annFUN2.4470.1062.775
classicCount-class0.0010.0000.001
classicExpr-class0.0020.0010.003
classicScore-class0.0050.0000.005
dagFunctions0.0010.0000.001
diagnosticMethods0.3640.0140.378
elimExpr-class0.0020.0010.002
elimScore-class0.0010.0000.001
geneList0.0040.0010.005
getPvalues3.0880.1163.221
getSigGroups4.3970.0764.474
groupGOTerms0.4530.0150.468
inducedGraph0.0500.0000.051
parentChild-class0.0030.0000.003
printGraph-methods0.0010.0000.001
topGOdata-class7.9960.1468.180
topGOresult-class0.1470.0020.149