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BioC 3.4: CHECK report for RedeR on moscato1

This page was generated on 2016-09-21 03:43:32 -0700 (Wed, 21 Sep 2016).

Package 1000/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RedeR 1.21.0
Mauro Castro
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/RedeR
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: RedeR
Version: 1.21.0
Command: rm -rf RedeR.buildbin-libdir RedeR.Rcheck && mkdir RedeR.buildbin-libdir RedeR.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RedeR.buildbin-libdir RedeR_1.21.0.tar.gz >RedeR.Rcheck\00install.out 2>&1 && cp RedeR.Rcheck\00install.out RedeR-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=RedeR.buildbin-libdir --install="check:RedeR-install.out" --force-multiarch --no-vignettes --timings RedeR_1.21.0.tar.gz
StartedAt: 2016-09-20 15:04:11 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 15:05:20 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 68.9 seconds
RetCode: 0
Status:  OK  
CheckDir: RedeR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf RedeR.buildbin-libdir RedeR.Rcheck && mkdir RedeR.buildbin-libdir RedeR.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RedeR.buildbin-libdir RedeR_1.21.0.tar.gz >RedeR.Rcheck\00install.out 2>&1 && cp RedeR.Rcheck\00install.out RedeR-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=RedeR.buildbin-libdir --install="check:RedeR-install.out" --force-multiarch --no-vignettes --timings RedeR_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/RedeR.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RedeR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RedeR' version '1.21.0'
* 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 whether package 'RedeR' can be installed ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
att.sete: no visible global function definition for 'grey'
att.sete : colorcategory: no visible global function definition for
  'grey'
att.sete : colorcategory: no visible global function definition for
  'colorRampPalette'
att.sete : colorscale1: no visible global function definition for
  'quantile'
att.sete : colorscale1: no visible global function definition for
  'grey'
att.sete : colorscale1: no visible global function definition for
  'colorRampPalette'
att.sete : colorscale2: no visible global function definition for
  'quantile'
att.sete : colorscale2: no visible global function definition for
  'grey'
att.sete : colorscale2: no visible global function definition for
  'colorRampPalette'
att.sete : xscale: no visible global function definition for 'quantile'
att.setv: no visible global function definition for 'grey'
att.setv : colorcategory: no visible global function definition for
  'grey'
att.setv : colorcategory: no visible global function definition for
  'colorRampPalette'
att.setv : colorscale1: no visible global function definition for
  'quantile'
att.setv : colorscale1: no visible global function definition for
  'grey'
att.setv : colorscale1: no visible global function definition for
  'colorRampPalette'
att.setv : colorscale2: no visible global function definition for
  'quantile'
att.setv : colorscale2: no visible global function definition for
  'grey'
att.setv : colorscale2: no visible global function definition for
  'colorRampPalette'
att.setv : xscale: no visible global function definition for 'quantile'
cea: no visible global function definition for 'cor'
cea: no visible global function definition for 'txtProgressBar'
cea: no visible global function definition for 'density'
cea: no visible global function definition for 'setTxtProgressBar'
cea: no visible global function definition for 'p.adjust'
cea : ptcea: no visible global function definition for 'density'
cea : ptcea: no visible global function definition for 'hist'
cea : ptcea: no visible global function definition for 'plot'
cea : ptcea: no visible global function definition for 'polygon'
cea : ptcea: no visible global function definition for 'lines'
cea : ptcea: no visible global function definition for 'legend'
cea : ptcea: no visible global function definition for 'rect'
gtoy.rm : nver: no visible global function definition for 'runif'
gtoy.rm: no visible global function definition for 'runif'
gtoy.rm: no visible global function definition for 'terrain.colors'
addGraph,RedPort: no visible global function definition for
  'colorRampPalette'
addLegend.color,RedPort: no visible global function definition for
  'colorRampPalette'
addLegend.shape,RedPort: no visible global function definition for
  'colorRampPalette'
addLegend.size,RedPort: no visible global function definition for
  'colorRampPalette'
calld,RedPort : testInterface: no visible global function definition
  for 'txtProgressBar'
calld,RedPort : testInterface: no visible global function definition
  for 'setTxtProgressBar'
nestNodes,RedPort: no visible global function definition for
  'colorRampPalette'
nesthc,RedPort: no visible global function definition for
  'colorRampPalette'
nesthc,RedPort: no visible global function definition for 'plot'
nesthc,RedPort: no visible global function definition for 'par'
nesthc,RedPort: no visible global function definition for 'text'
nesthc,RedPort: no visible global function definition for 'rect'
Undefined global functions or variables:
  colorRampPalette cor density grey hist legend lines p.adjust par plot
  polygon quantile rect runif setTxtProgressBar terrain.colors text
  txtProgressBar
Consider adding
  importFrom("grDevices", "colorRampPalette", "grey", "terrain.colors")
  importFrom("graphics", "hist", "legend", "lines", "par", "plot",
             "polygon", "rect", "text")
  importFrom("stats", "cor", "density", "p.adjust", "quantile", "runif")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
* 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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
  'D:/biocbld/bbs-3.4-bioc/meat/RedeR.Rcheck/00check.log'
for details.


RedeR.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'RedeR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RedeR' as RedeR_1.21.0.zip
* DONE (RedeR)

RedeR.Rcheck/examples_i386/RedeR-Ex.timings:

nameusersystemelapsed
RedPort-class000
RedPort000
RedeR.data0.570.050.61
addEdgeBetweenContainers000
addEdges000
addGraph000
addLegend000
addNodes0.010.000.02
addSeries000
addSubgraph000
addSubgraph.list000
att0.100.000.09
calld000
cea0.060.000.06
deSelectEdges000
deSelectGraph000
deSelectNodes0.010.000.02
deleteEdges000
deleteNodes000
deleteSelectedEdges000
deleteSelectedNodes000
duplicateGraph000
exitd000
getContainerComponets0.020.000.01
getEdgeIDs000
getEdges000
getGraph000
getNodeIDs000
getNodes000
getSourceEdgeIDs000
getTargetEdgeIDs0.010.000.02
gtoy.rm000
isDynamicsActive000
mergeNodes000
mergeOutEdges000
nestNodes000
nesthc000
ping000
relax0.000.010.01
resetd000
selectAllEdges000
selectAllNodes000
selectEdges000
selectGraph000
selectNodes000
setArrowDirection000
subg0.090.000.09
updateContainerSize000
updateGraph000
version000

RedeR.Rcheck/examples_x64/RedeR-Ex.timings:

nameusersystemelapsed
RedPort-class000
RedPort000
RedeR.data0.530.030.56
addEdgeBetweenContainers000
addEdges000
addGraph0.020.000.02
addLegend000
addNodes000
addSeries000
addSubgraph000
addSubgraph.list000
att0.080.010.09
calld000
cea0.040.000.04
deSelectEdges000
deSelectGraph0.020.000.02
deSelectNodes000
deleteEdges000
deleteNodes000
deleteSelectedEdges000
deleteSelectedNodes000
duplicateGraph000
exitd0.020.000.01
getContainerComponets000
getEdgeIDs000
getEdges000
getGraph000
getNodeIDs000
getNodes000
getSourceEdgeIDs000
getTargetEdgeIDs000
gtoy.rm000
isDynamicsActive000
mergeNodes000
mergeOutEdges000
nestNodes000
nesthc000
ping000
relax0.000.000.03
resetd000
selectAllEdges000
selectAllNodes000
selectEdges000
selectGraph0.010.000.01
selectNodes000
setArrowDirection000
subg0.10.00.1
updateContainerSize000
updateGraph000
version000