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BioC 3.1: CHECK report for CompGO on zin2

This page was generated on 2015-10-09 09:26:02 -0700 (Fri, 09 Oct 2015).

Package 206/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CompGO 1.4.0
Ashley J. Waardenberg
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/CompGO
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CompGO
Version: 1.4.0
Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings CompGO_1.4.0.tar.gz
StartedAt: 2015-10-08 23:53:15 -0700 (Thu, 08 Oct 2015)
EndedAt: 2015-10-08 23:58:47 -0700 (Thu, 08 Oct 2015)
EllapsedTime: 332.2 seconds
RetCode: 0
Status:  OK 
CheckDir: CompGO.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings CompGO_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/CompGO.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 ‘CompGO/DESCRIPTION’ ... OK
* this is package ‘CompGO’ version ‘1.4.0’
* 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 ... [21s/31s] 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 ... [22s/29s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
plotTwoGODags 7.113  0.038   9.327
* 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-3.1-bioc/meat/CompGO.Rcheck/00check.log’
for details.


CompGO.Rcheck/00install.out:

* installing *source* package ‘CompGO’ ...
** R
** data
** 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 (CompGO)

CompGO.Rcheck/CompGO-Ex.timings:

nameusersystemelapsed
annotateBedFromDb2.3690.0233.186
compareZscores0.0950.0000.248
doZtrans.single0.0060.0000.006
getFnAnot_genome0.0000.0000.001
plotPairwise0.3590.0040.381
plotTwoGODags7.1130.0389.327
plotZRankedDAG0.0010.0000.001
plotZScores1.0810.0001.604
slidingJaccard0.0540.0000.055
viewKegg0.0010.0000.000
zTransformDirectory0.0010.0000.001