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BioC 3.0: CHECK report for RamiGO on zin1

This page was generated on 2015-04-10 09:39:29 -0700 (Fri, 10 Apr 2015).

Package 713/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RamiGO 1.12.1
Markus Schroeder
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/RamiGO
Last Changed Rev: 100640 / Revision: 102249
Last Changed Date: 2015-03-13 07:08:14 -0700 (Fri, 13 Mar 2015)
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: RamiGO
Version: 1.12.1
Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings RamiGO_1.12.1.tar.gz
StartedAt: 2015-04-10 03:28:55 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 03:30:05 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 69.8 seconds
RetCode: 0
Status:  OK 
CheckDir: RamiGO.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings RamiGO_1.12.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/RamiGO.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘1.12.1’
* 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 ... [4s/4s] 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 ... NOTE
Package in Depends field not imported from: ‘gsubfn’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
readAmigoDot : <anonymous>: no visible global function definition for
  ‘strapply’
* 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 files in ‘vignettes’ ... OK
* checking examples ... [9s/25s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
getAmigoTree 2.228  0.124   8.451
* 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 were 2 notes.
See
  ‘/home/biocbuild/bbs-3.0-bioc/meat/RamiGO.Rcheck/00check.log’
for details.

RamiGO.Rcheck/00install.out:

* installing *source* package ‘RamiGO’ ...
** R
** data
** inst
** preparing package for lazy loading
Note: the specification for S3 class “AsIs” in package ‘XMLRPC’ seems equivalent to one from package ‘BiocGenerics’: 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
Note: the specification for S3 class “AsIs” in package ‘XMLRPC’ seems equivalent to one from package ‘BiocGenerics’: not turning on duplicate class definitions for this class.
* DONE (RamiGO)

RamiGO.Rcheck/RamiGO-Ex.timings:

nameusersystemelapsed
AmigoDot-class0.0000.0000.002
AmigoDot0.6720.0562.146
AmigoDot.to.Cyto0.5280.0041.941
AmigoDot.to.graphAM0.5440.0082.009
AmigoDot.to.graphNEL0.6200.0042.060
adjM2gml0.7400.0402.117
c5.go.mapping0.0080.0000.011
exportCytoGML0.6680.0362.051
getAmigoTree2.2280.1248.451
readAmigoDot0.6000.0522.067