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BioC 2.12: CHECK report for RamiGO on george2

This page was generated on 2013-10-09 09:37:46 -0700 (Wed, 09 Oct 2013).

Package 518/671HostnameOS / ArchBUILDCHECKBUILD BIN
RamiGO 1.6.0
Markus Schroeder
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/RamiGO
Last Changed Rev: 75263 / Revision: 81334
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: RamiGO
Version: 1.6.0
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings RamiGO_1.6.0.tar.gz
StartedAt: 2013-10-09 04:21:07 -0700 (Wed, 09 Oct 2013)
EndedAt: 2013-10-09 04:22:59 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 111.9 seconds
RetCode: 0
Status:  OK 
CheckDir: RamiGO.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/RamiGO.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RamiGO/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RamiGO’ 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 ‘RamiGO’ can be installed ... [8s/9s] OK
* checking installed package size ... OK
* checking package 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 for unstated 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 ... OK
* 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 installed files from ‘inst/doc’ ... OK
* checking examples ... [9s/24s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
getAmigoTree 2.116  0.168   9.964
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

RamiGO.Rcheck/00install.out:

* installing *source* package ‘RamiGO’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning in .simpleDuplicateClass(def, prev) :
  the specification for S3 class “AsIs” in package ‘XMLRPC’ seems equivalent to one from package ‘BiocGenerics’ and is not turning on duplicate class definitions for this class
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in .simpleDuplicateClass(def, prev) :
  the specification for S3 class “AsIs” in package ‘XMLRPC’ seems equivalent to one from package ‘BiocGenerics’ and is not turning on duplicate class definitions for this class
* DONE (RamiGO)

RamiGO.Rcheck/RamiGO-Ex.timings:

nameusersystemelapsed
AmigoDot-class0.0200.0000.022
AmigoDot0.4680.0121.834
AmigoDot.to.Cyto0.0120.0000.015
AmigoDot.to.graphAM0.2360.0121.507
AmigoDot.to.graphNEL0.3560.0161.631
adjM2gml0.2720.0241.561
c5.go.mapping0.0760.0040.081
exportCytoGML0.3000.0241.594
getAmigoTree2.1160.1689.964
readAmigoDot0.2640.0201.549