pcaGoPromoter 1.20.0
Morten Hansen
| Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/pcaGoPromoter | | Last Changed Rev: 129126 / Revision: 131943 | | Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings pcaGoPromoter_1.20.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/pcaGoPromoter.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pcaGoPromoter/DESCRIPTION’ ... OK
* this is package ‘pcaGoPromoter’ version ‘1.20.0’
* 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 ‘pcaGoPromoter’ 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls in package code:
‘GO.db’ ‘Rgraphviz’ ‘parallel’ ‘pcaGoPromoter.Hs.hg19’
‘pcaGoPromoter.Mm.mm9’ ‘pcaGoPromoter.Rn.rn4’
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in 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
dropVarNull: no visible global function definition for ‘var’
dropVarNull: no visible global function definition for ‘na.omit’
getMatricesWithHits: no visible global function definition for
‘fisher.test’
getMatricesWithHits: no visible global function definition for
‘p.adjust’
getSigGOTermsOnce: no visible global function definition for
‘fisher.test’
getSigGOTermsOnce : <anonymous>: no visible global function definition
for ‘binom.test’
getSigGOTermsOnce: no visible global function definition for ‘p.adjust’
leaveOutFindPvalues : <anonymous>: no visible global function
definition for ‘median’
makeGOtreeRgraphviz: no visible global function definition for ‘new’
makeGOtreeRgraphviz: no visible global function definition for ‘rgb’
makeGOtreeRgraphviz: no visible global function definition for
‘addNode’
makeGOtreeRgraphviz: no visible global function definition for
‘addEdge’
makeGOtreeRgraphviz: no visible global function definition for ‘nodes’
makeGOtreeRgraphviz: no visible global function definition for
‘nodeRenderInfo<-’
makeGOtreeRgraphviz: no visible global function definition for
‘edgeRenderInfo<-’
makeGOtreeRgraphviz: no visible global function definition for
‘parRenderInfo<-’
makeGOtreeRgraphviz: no visible global function definition for ‘par’
makeGOtreeRgraphviz: no visible global function definition for
‘renderGraph’
makeGOtreeRgraphviz: no visible global function definition for
‘layoutGraph’
makeGOtreeRgraphviz: no visible global function definition for ‘legend’
newSearchGOtreeForTerms: no visible binding for global variable
‘GOBPANCESTOR’
pca: no visible global function definition for ‘annotation’
pca: no visible global function definition for ‘exprs’
pca: no visible global function definition for ‘var’
pca: no visible global function definition for ‘na.omit’
pca: no visible global function definition for ‘prcomp’
pcaInfoPlot: no visible global function definition for ‘plot’
plot.pca: no visible global function definition for ‘par’
plot.pca: no visible global function definition for ‘layout’
plot.pca: no visible global function definition for ‘var’
plot.pca: no visible global function definition for ‘plot’
plot.pca: no visible global function definition for ‘polygon’
plot.pca: no visible global function definition for ‘lines’
plot.pca: no visible global function definition for ‘points’
plot.pca: no visible global function definition for ‘abline’
plot.pca: no visible global function definition for ‘box’
plot.pca: no visible global function definition for ‘text’
plot.pca: no visible global function definition for ‘plot.new’
plot.pca: no visible global function definition for ‘legend’
primo: no visible global function definition for ‘data’
primoData.getPromoters: no visible global function definition for
‘readFASTA’
primoHits: no visible global function definition for ‘data’
printAnnText: no visible global function definition for ‘mtext’
printAnnotation: no visible global function definition for ‘mtext’
Undefined global functions or variables:
GOBPANCESTOR abline addEdge addNode annotation binom.test box data
edgeRenderInfo<- exprs fisher.test layout layoutGraph legend lines
median mtext na.omit new nodeRenderInfo<- nodes p.adjust par
parRenderInfo<- plot plot.new points polygon prcomp readFASTA
renderGraph rgb text var
Consider adding
importFrom("grDevices", "rgb")
importFrom("graphics", "abline", "box", "layout", "legend", "lines",
"mtext", "par", "plot", "plot.new", "points", "polygon",
"text")
importFrom("methods", "new")
importFrom("stats", "binom.test", "fisher.test", "median", "na.omit",
"p.adjust", "prcomp", "var")
importFrom("utils", "data")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
GOtree 59.972 0.564 61.510
primo 16.704 0.136 17.335
* 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: 2 NOTEs
See
‘/home/biocbuild/bbs-3.5-bioc/meat/pcaGoPromoter.Rcheck/00check.log’
for details.