BioC 3.4: CHECK report for rGREAT on zin1

Package: rGREAT

Version: 1.5.2

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings rGREAT_1.5.2.tar.gz

StartedAt: 2016-09-20 11:44:48 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 11:46:11 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 82.5 seconds

RetCode: 0

Status:  OK

CheckDir: rGREAT.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings rGREAT_1.5.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/rGREAT.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rGREAT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rGREAT’ version ‘1.5.2’
* 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 ‘rGREAT’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotRegionGeneAssociationGraphs,GreatJob: no visible global function
  definition for ‘barplot’
plotRegionGeneAssociationGraphs,GreatJob: no visible global function
  definition for ‘text’
plotRegionGeneAssociationGraphs,GreatJob: no visible global function
  definition for ‘legend’
plotRegionGeneAssociationGraphs,GreatJob: no visible global function
  definition for ‘axis’
plotRegionGeneAssociationGraphs,GreatJob: no visible global function
  definition for ‘par’
plotRegionGeneAssociationGraphs,GreatJob: no visible global function
  definition for ‘lines’
plotRegionGeneAssociationGraphs,GreatJob: no visible global function
  definition for ‘arrows’
Undefined global functions or variables:
  arrows axis barplot legend lines par text
Consider adding
  importFrom("graphics", "arrows", "axis", "barplot", "legend", "lines",
             "par", "text")
to your NAMESPACE file.
* 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
submitGreatJob 0.24  0.012  12.599
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’
 OK
* 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 NOTE
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/rGREAT.Rcheck/00check.log’
for details.

* installing *source* package ‘rGREAT’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (rGREAT)

name	user	system	elapsed
GreatJob-class	0	0	0
availableCategories-GreatJob-method	0.036	0.000	0.034
availableOntologies-GreatJob-method	0.028	0.004	0.032
getEnrichmentTables-GreatJob-method	0.076	0.000	0.077
plotRegionGeneAssociationGraphs-GreatJob-method	0.304	0.004	0.306
submitGreatJob	0.240	0.012	12.599