BioC 3.1: CHECK report for pcaGoPromoter on zin2

Package: pcaGoPromoter

Version: 1.12.0

Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings pcaGoPromoter_1.12.0.tar.gz

StartedAt: 2015-10-09 04:12:38 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 04:15:14 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 156.1 seconds

RetCode: 0

Status:  OK

CheckDir: pcaGoPromoter.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings pcaGoPromoter_1.12.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/pcaGoPromoter.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.12.0’
* 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 ... [5s/5s] 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’ ‘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.
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 ... [98s/98s] OK
Examples with CPU or elapsed time > 5s
         user system elapsed
GOtree 59.053  0.547  59.719
primo  32.622  0.140  32.778
* 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-3.1-bioc/meat/pcaGoPromoter.Rcheck/00check.log’
for details.

* installing *source* package ‘pcaGoPromoter’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (pcaGoPromoter)

name	user	system	elapsed
GOtree	59.053	0.547	59.719
pca	2.662	0.000	2.659
pcaGoPromoter-package	0.000	0.000	0.001
primo	32.622	0.140	32.778
primoData	0	0	0