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BioC 3.0: CHECK report for CompGO on oaxaca

This page was generated on 2015-04-10 10:08:48 -0700 (Fri, 10 Apr 2015).

Package 192/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CompGO 1.2.0
Ashley J. Waardenberg
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/CompGO
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 

Summary

Package: CompGO
Version: 1.2.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch CompGO_1.2.0.tar.gz
StartedAt: 2015-04-09 22:33:10 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 22:41:16 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 486.2 seconds
RetCode: 0
Status:  OK 
CheckDir: CompGO.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch CompGO_1.2.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/CompGO.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CompGO/DESCRIPTION’ ... OK
* this is package ‘CompGO’ version ‘1.2.0’
* 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 ... [44s/44s] 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’
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 ... [39s/39s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
plotTwoGODags     8.796  0.163   9.005
annotateBedFromDb 5.288  0.083   5.413
* 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 was 1 note.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/CompGO.Rcheck/00check.log’
for details.

CompGO.Rcheck/00install.out:

* 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)

CompGO.Rcheck/CompGO-Ex.timings:

nameusersystemelapsed
annotateBedFromDb5.2880.0835.413
compareZscores0.1370.0110.297
doZtrans.single0.0090.0050.014
getFnAnot_genome0.0010.0000.001
plotPairwise1.0620.0181.081
plotTwoGODags8.7960.1639.005
plotZRankedDAG0.0000.0000.001
plotZScores1.8140.0161.860
slidingJaccard0.1090.0130.122
viewKegg0.0010.0010.001
zTransformDirectory0.0010.0000.001