BioC 2.14: CHECK report for CompGO on morelia

Package: CompGO

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch CompGO_1.0.0.tar.gz

StartedAt: 2014-10-07 22:09:14 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 22:16:09 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 415.6 seconds

RetCode: 0

Status:  OK

CheckDir: CompGO.Rcheck

Warnings: 0

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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 CompGO_1.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/CompGO.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CompGO/DESCRIPTION’ ... OK
* this is package ‘CompGO’ version ‘1.0.0’
* 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 ... [36s/37s] 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 ‘Z’
plotRankedZDAG: no visible binding for global variable ‘cutoff’
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [39s/39s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
plotTwoGODags 10.655  0.168  10.834
* 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

NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-2.14-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	4.667	0.096	4.900
doZtrans.single	0.012	0.009	0.061
getFnAnot_genome	0.001	0.000	0.001
plotPairwise	0.643	0.027	0.671
plotTwoGODags	10.655	0.168	10.834
plotZScores	1.725	0.016	1.820
slidingJaccard	0.088	0.011	0.099
zTransformDirectory	0.001	0.000	0.000