BioC 3.2: CHECK report for CompGO on perceval

Package: CompGO

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CompGO_1.6.0.tar.gz

StartedAt: 2015-11-10 03:38:00 -0800 (Tue, 10 Nov 2015)

EndedAt: 2015-11-10 03:44:00 -0800 (Tue, 10 Nov 2015)

EllapsedTime: 359.8 seconds

RetCode: 0

Status:  OK

CheckDir: CompGO.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CompGO_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/CompGO.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 ‘CompGO/DESCRIPTION’ ... OK
* this is package ‘CompGO’ version ‘1.6.0’
* 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 ‘CompGO’ can be installed ... [33s/34s] 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
doZtrans.single: no visible binding for global variable ‘Term’
doZtrans.single: no visible binding for global variable ‘Z’
plotInteractive: no visible binding for global variable ‘Var1’
plotInteractive: no visible binding for global variable ‘Var2’
plotInteractive: no visible binding for global variable ‘value’
plotTwoGODags: no visible global function definition for ‘goDag’
plotTwoGODags: no visible global function definition for ‘nodes’
plotTwoGODags: no visible global function definition for
  ‘nodeRenderInfo<-’
plotZRankedDAG: no visible global function definition for ‘goDag’
plotZRankedDAG: no visible global function definition for ‘nodes’
plotZRankedDAG: no visible global function definition for
  ‘nodeRenderInfo<-’
slidingJaccard: no visible binding for global variable ‘useRawPvals’
* 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [30s/30s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
plotTwoGODags 9.415  0.232   9.664
* 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
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/CompGO.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
annotateBedFromDb	0.866	0.035	0.900
compareZscores	0.123	0.011	0.165
doZtrans.single	0.007	0.004	0.011
getFnAnot_genome	0.001	0.001	0.001
plotPairwise	0.502	0.012	0.514
plotTwoGODags	9.415	0.232	9.664
plotZRankedDAG	0	0	0
plotZScores	1.609	0.008	1.617
slidingJaccard	0.080	0.005	0.086
viewKegg	0.000	0.000	0.001
zTransformDirectory	0.000	0.000	0.001