BioC 3.5: CHECK report for topGO on oaxaca
This page was generated on 2017-03-04 16:35:01 -0500 (Sat, 04 Mar 2017).
topGO 2.27.0 Adrian Alexa
Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017) | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/topGO | Last Changed Rev: 122712 / Revision: 127142 | Last Changed Date: 2016-10-17 15:10:43 -0400 (Mon, 17 Oct 2016) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | |
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |
toluca2 | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | [ OK ] | OK | |
Summary
Package: topGO |
Version: 2.27.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings topGO_2.27.0.tar.gz |
StartedAt: 2017-03-04 10:05:25 -0800 (Sat, 04 Mar 2017) |
EndedAt: 2017-03-04 10:07:42 -0800 (Sat, 04 Mar 2017) |
EllapsedTime: 136.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: topGO.Rcheck |
Warnings: 0 |
Command output
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings topGO_2.27.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/topGO.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘2.27.0’
* 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 ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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:
‘Rgraphviz’ ‘multtest’
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
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
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’
getPvalues: no visible global function definition for ‘mt.teststat’
getPvalues: no visible global function definition for ‘mt.rawp2adjp’
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: no visible global function definition for
‘error’
scoresInTerm,topGOdata-missing: no visible global function definition
for ‘scoreInNode’
Undefined global functions or variables:
.PERMSUM.LOOKUP .PERMSUM.MAT AgNode agopen drawTxtLabel error
getDefaultAttrs getNodeCenter getNodeLW getNodeXY getX getY
mt.rawp2adjp mt.teststat name pieGlyph scoreInNode toDot txtLabel
* 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 ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
topGOdata-class 6.879 0.258 7.185
* 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: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.5-bioc/meat/topGO.Rcheck/00check.log’
for details.
topGO.Rcheck/00install.out:
* installing *source* package ‘topGO’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.
* DONE (topGO)
topGO.Rcheck/topGO-Ex.timings:
name | user | system | elapsed
|
GOdata | 0.252 | 0.006 | 0.259 |
|
annFUN | 1.864 | 0.091 | 2.066 |
|
classicCount-class | 0.001 | 0.000 | 0.001 |
|
classicExpr-class | 0.002 | 0.000 | 0.003 |
|
classicScore-class | 0.005 | 0.000 | 0.005 |
|
dagFunctions | 0.000 | 0.000 | 0.001 |
|
diagnosticMethods | 0.472 | 0.008 | 0.481 |
|
elimExpr-class | 0.001 | 0.000 | 0.002 |
|
elimScore-class | 0.001 | 0.000 | 0.000 |
|
geneList | 0.002 | 0.001 | 0.004 |
|
getPvalues | 4.220 | 0.163 | 4.468 |
|
getSigGroups | 4.195 | 0.051 | 4.250 |
|
groupGOTerms | 0.497 | 0.008 | 0.505 |
|
inducedGraph | 0.126 | 0.002 | 0.128 |
|
parentChild-class | 0.003 | 0.000 | 0.003 |
|
printGraph-methods | 0.000 | 0.000 | 0.001 |
|
topGOdata-class | 6.879 | 0.258 | 7.185 |
|
topGOresult-class | 0.068 | 0.002 | 0.070 |
|