pcaGoPromoter 1.10.0
Morten Hansen
| Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/pcaGoPromoter | | Last Changed Rev: 95439 / Revision: 102249 | | Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | NotNeeded | OK | OK | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | [ OK ] | OK |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | 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 --no-multiarch pcaGoPromoter_1.10.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/pcaGoPromoter.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pcaGoPromoter/DESCRIPTION’ ... OK
* this is package ‘pcaGoPromoter’ version ‘1.10.0’
* 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 ... [13s/13s] 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' call to ‘ellipse’ which was already attached by Depends.
Please remove these calls from your code.
'library' or 'require' calls in package code:
‘Biostrings’ ‘GO.db’ ‘parallel’ ‘pcaGoPromoter.Hs.hg19’
‘pcaGoPromoter.Mm.mm9’ ‘pcaGoPromoter.Rn.rn4’ ‘Rgraphviz’
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespace in Imports field not imported from: ‘Biobase’
All declared Imports should be used.
Package in Depends field not imported from: ‘ellipse’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
convertInput: no visible global function definition for ‘keys’
getGOidsInOntology: no visible global function definition for
‘mappedkeys’
getGOsDownTree: no visible binding for global variable ‘GOTERM’
getGOsDownTree : <anonymous>: no visible global function definition for
‘Term’
getGOsDownTree : <anonymous>: no visible global function definition for
‘GOID’
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
‘renderGraph’
makeGOtreeRgraphviz: no visible global function definition for
‘layoutGraph’
newSearchGOtreeForTerms: no visible binding for global variable
‘GOBPANCESTOR’
pca: no visible global function definition for ‘annotation’
pca: no visible global function definition for ‘exprs’
pcaLeaveOut: no visible global function definition for ‘mclapply’
plot.pca: no visible global function definition for ‘ellipse’
primoData.getAllThresholds: no visible global function definition for
‘mclapply’
primoData.getPromoters: no visible global function definition for
‘readFASTA’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [223s/224s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
GOtree 125.348 8.941 134.564
primo 62.379 16.114 78.759
* 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
NOTE: There were 2 notes.
See
‘/Users/biocbuild/bbs-3.0-bioc/meat/pcaGoPromoter.Rcheck/00check.log’
for details.