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BioC 3.2: CHECK report for RedeR on perceval

This page was generated on 2015-10-27 17:34:40 -0400 (Tue, 27 Oct 2015).

Package 864/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RedeR 1.18.0
Mauro Castro
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/RedeR
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: RedeR
Version: 1.18.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RedeR_1.18.0.tar.gz
StartedAt: 2015-10-27 11:33:27 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 11:34:21 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 53.4 seconds
RetCode: 0
Status:  OK 
CheckDir: RedeR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RedeR_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/RedeR.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RedeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RedeR’ version ‘1.18.0’
* 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 ‘RedeR’ can be installed ... [4s/4s] OK
* checking installed package size ... NOTE
  installed size is  8.8Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    java   4.3Mb
* 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 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
addSubgraph,RedPort : .local: no visible global function definition for
  ‘G<-’
addSubgraph.list,RedPort : .local: no visible global function
  definition for ‘G<-’
nesthc,RedPort : .local: no visible global function definition for
  ‘pvpick’
* 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 ... [2s/2s] OK
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/RedeR.Rcheck/00check.log’
for details.


RedeR.Rcheck/00install.out:

* installing *source* package ‘RedeR’ ...
** 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 (RedeR)

RedeR.Rcheck/RedeR-Ex.timings:

nameusersystemelapsed
RedPort-class0.0020.0000.002
RedPort0.0010.0000.001
RedeR.data0.6450.0380.683
addEdgeBetweenContainers0.0050.0000.005
addEdges0.0010.0010.002
addGraph0.0020.0000.003
addLegend0.0020.0000.002
addNodes0.0010.0000.001
addSeries0.0010.0000.001
addSubgraph0.0020.0010.002
addSubgraph.list0.0020.0000.002
att0.1020.0080.109
calld0.0020.0000.001
cea0.0660.0050.071
deSelectEdges0.0010.0000.001
deSelectGraph0.0020.0000.001
deSelectNodes0.0010.0000.001
deleteEdges0.0020.0000.002
deleteNodes0.0020.0000.002
deleteSelectedEdges0.0010.0010.002
deleteSelectedNodes0.0020.0000.002
duplicateGraph0.0010.0000.002
exitd0.0020.0010.001
getContainerComponets0.0020.0000.002
getEdgeIDs0.0020.0000.001
getEdges0.0010.0000.002
getGraph0.0020.0000.001
getNodeIDs0.0020.0000.002
getNodes0.0020.0000.001
getSourceEdgeIDs0.0030.0000.003
getTargetEdgeIDs0.0020.0010.003
gtoy.rm000
isDynamicsActive0.0010.0000.001
mergeNodes0.0020.0000.001
mergeOutEdges0.0020.0000.002
nestNodes0.0010.0010.002
nesthc0.0010.0000.001
ping0.0020.0000.002
relax0.0020.0000.002
resetd0.0010.0000.001
selectAllEdges0.0010.0000.002
selectAllNodes0.0020.0000.001
selectEdges0.0010.0000.002
selectGraph0.0010.0000.002
selectNodes0.0020.0000.002
setArrowDirection0.0020.0000.002
subg0.1050.0110.116
updateContainerSize0.0020.0000.002
updateGraph0.0010.0010.002
version0.0020.0000.002