topGO 2.22.0
Adrian Alexa
| Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/topGO | | Last Changed Rev: 109589 / Revision: 109947 | | Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015) |
| linux1.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |  |
| windows1.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | WARNINGS | OK | |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | [ WARNINGS ] | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | WARNINGS | OK | |
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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_2.22.0.tar.gz
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* 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 ... [26s/26s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
topGOdata-class 8.434 0.147 8.607
* 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.
* 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)