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CHECK report for RCyjs on tokay1

This page was generated on 2019-04-13 11:25:14 -0400 (Sat, 13 Apr 2019).

Package 1270/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RCyjs 2.4.0
Paul Shannon
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/RCyjs
Branch: RELEASE_3_8
Last Commit: 205545f
Last Changed Date: 2018-10-30 11:41:57 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: RCyjs
Version: 2.4.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RCyjs.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings RCyjs_2.4.0.tar.gz
StartedAt: 2019-04-13 04:54:56 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 04:56:45 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 108.7 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: RCyjs.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RCyjs.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings RCyjs_2.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/RCyjs.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RCyjs/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RCyjs' version '2.4.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 'RCyjs' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.2Mb
  sub-directories of 1Mb or more:
    browserCode   3.0Mb
    doc           1.1Mb
* 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 ... 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 include directives in Makefiles ... 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 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... WARNING
Package vignette without corresponding PDF/HTML:
   'RCyjs.Rmd'

* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/RCyjs.Rcheck/00check.log'
for details.



Installation output

RCyjs.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/RCyjs_2.4.0.tar.gz && rm -rf RCyjs.buildbin-libdir && mkdir RCyjs.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RCyjs.buildbin-libdir RCyjs_2.4.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL RCyjs_2.4.0.zip && rm RCyjs_2.4.0.tar.gz RCyjs_2.4.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1857k  100 1857k    0     0  18.2M      0 --:--:-- --:--:-- --:--:-- 18.8M

install for i386

* installing *source* package 'RCyjs' ...
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'layout' in package 'RCyjs'
** help
*** installing help indices
  converting help for package 'RCyjs'
    finding HTML links ... done
    RCyjs-class                             html  
    addGraph                                html  
    addGraphFromFile                        html  
    clearSelection                          html  
    createTestGaph                          html  
    deleteGraph                             html  
    deleteSelectedNodes                     html  
    eda                                     html  
    edaNames                                html  
    fit                                     html  
    fitSelection                            html  
    getEdgeCount                            html  
    getJSON                                 html  
    getLayoutStrategies                     html  
    getNodeCount                            html  
    getNodes                                html  
    getPosition                             html  
    getSelectedNodes                        html  
    getSupportedEdgeDecoratorShapes         html  
    getSupportedNodeShapes                  html  
    getZoom                                 html  
    hAlign                                  html  
    hideAllEdges                            html  
    hideEdges                               html  
    hideSelectedNodes                       html  
    invertNodeSelection                     html  
    layout                                  html  
    layoutSelectionInGrid                   html  
    layoutSelectionInGridInferAnchorm       html  
    loadStyleFile                           html  
    noa                                     html  
    noaNames                                html  
    redraw                                  html  
    restoreLayout                           html  
    saveJPG                                 html  
    saveLayout                              html  
    savePNG                                 html  
    selectFirstNeighborsOfSelectedNodes     html  
    selectNodes                             html  
    setBackgroundColor                      html  
    setDefaultEdgeColor                     html  
    setDefaultEdgeLineColor                 html  
    setDefaultEdgeLineStyle                 html  
    setDefaultEdgeSourceArrowColor          html  
    setDefaultEdgeSourceArrowShape          html  
    setDefaultEdgeTargetArrowColor          html  
    setDefaultEdgeTargetArrowShape          html  
    setDefaultEdgeWidth                     html  
    setDefaultNodeBorderColor               html  
    setDefaultNodeBorderWidth               html  
    setDefaultNodeColor                     html  
    setDefaultNodeFontColor                 html  
    setDefaultNodeFontSize                  html  
    setDefaultNodeHeight                    html  
    setDefaultNodeShape                     html  
    setDefaultNodeSize                      html  
    setDefaultNodeWidth                     html  
    setDefaultStyle                         html  
    setEdgeAttributes                       html  
    setEdgeStyle                            html  
    setGraph                                html  
    setNodeAttributes                       html  
    setNodeBorderColor                      html  
    setNodeBorderWidth                      html  
    setNodeColor                            html  
    setNodeColorRule                        html  
    setNodeFontColor                        html  
    setNodeFontSize                         html  
    setNodeHeight                           html  
    setNodeLabelAlignment                   html  
    setNodeLabelRule                        html  
    setNodeShape                            html  
    setNodeSize                             html  
    setNodeSizeRule                         html  
    setNodeWidth                            html  
    setPosition                             html  
    setZoom                                 html  
    sfn                                     html  
    showAll                                 html  
    showEdges                               html  
    simpleDemoGraph                         html  
    vAlign                                  html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'RCyjs' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RCyjs' as RCyjs_2.4.0.zip
* DONE (RCyjs)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'RCyjs' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

RCyjs.Rcheck/tests_i386/runTests.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # disabled: the bioc build system no longer supports browser use.
> # BiocGenerics:::testPackage("RCyjs")
> 
> proc.time()
   user  system elapsed 
   0.26    0.01    0.26 

RCyjs.Rcheck/tests_x64/runTests.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # disabled: the bioc build system no longer supports browser use.
> # BiocGenerics:::testPackage("RCyjs")
> 
> proc.time()
   user  system elapsed 
   0.14    0.01    0.15 

Example timings

RCyjs.Rcheck/examples_i386/RCyjs-Ex.timings

nameusersystemelapsed
RCyjs-class000
addGraph000
addGraphFromFile000
clearSelection000
createTestGaph0.020.000.01
deleteGraph000
deleteSelectedNodes000
eda000
edaNames000
fit000
fitSelection000
getEdgeCount000
getJSON000
getLayoutStrategies000
getNodeCount000
getNodes000
getPosition000
getSelectedNodes000
getSupportedEdgeDecoratorShapes000
getSupportedNodeShapes000
getZoom000
hAlign000
hideAllEdges000
hideEdges000
hideSelectedNodes000
invertNodeSelection000
layout000
layoutSelectionInGrid000
layoutSelectionInGridInferAnchorm000
loadStyleFile000
noa000
noaNames000
redraw000
restoreLayout000
saveJPG000
saveLayout0.020.000.02
savePNG000
selectFirstNeighborsOfSelectedNodes000
selectNodes000
setBackgroundColor000
setDefaultEdgeColor000
setDefaultEdgeLineColor000
setDefaultEdgeLineStyle000
setDefaultEdgeSourceArrowColor000
setDefaultEdgeSourceArrowShape000
setDefaultEdgeTargetArrowColor000
setDefaultEdgeTargetArrowShape000
setDefaultEdgeWidth000
setDefaultNodeBorderColor000
setDefaultNodeBorderWidth000
setDefaultNodeColor000
setDefaultNodeFontColor000
setDefaultNodeFontSize000
setDefaultNodeHeight000
setDefaultNodeShape000
setDefaultNodeSize000
setDefaultNodeWidth000
setDefaultStyle000
setEdgeStyle000
setGraph000
setNodeAttributes000
setNodeBorderColor000
setNodeBorderWidth000
setNodeColor000
setNodeColorRule000
setNodeFontColor000
setNodeFontSize000
setNodeHeight000
setNodeLabelRule000
setNodeShape000
setNodeSize000
setNodeSizeRule000
setNodeWidth000
setPosition000
setZoom000
sfn000
showAll000
showEdges000
simpleDemoGraph0.080.000.07
vAlign000

RCyjs.Rcheck/examples_x64/RCyjs-Ex.timings

nameusersystemelapsed
RCyjs-class000
addGraph000
addGraphFromFile000
clearSelection000
createTestGaph000
deleteGraph000
deleteSelectedNodes000
eda000
edaNames000
fit000
fitSelection000
getEdgeCount000
getJSON000
getLayoutStrategies000
getNodeCount000
getNodes000
getPosition000
getSelectedNodes000
getSupportedEdgeDecoratorShapes000
getSupportedNodeShapes000
getZoom000
hAlign000
hideAllEdges000
hideEdges000
hideSelectedNodes000
invertNodeSelection000
layout000
layoutSelectionInGrid000
layoutSelectionInGridInferAnchorm000
loadStyleFile000
noa000
noaNames000
redraw000
restoreLayout000
saveJPG000
saveLayout000
savePNG000
selectFirstNeighborsOfSelectedNodes000
selectNodes000
setBackgroundColor000
setDefaultEdgeColor000
setDefaultEdgeLineColor000
setDefaultEdgeLineStyle000
setDefaultEdgeSourceArrowColor000
setDefaultEdgeSourceArrowShape000
setDefaultEdgeTargetArrowColor000
setDefaultEdgeTargetArrowShape000
setDefaultEdgeWidth000
setDefaultNodeBorderColor000
setDefaultNodeBorderWidth000
setDefaultNodeColor000
setDefaultNodeFontColor000
setDefaultNodeFontSize000
setDefaultNodeHeight000
setDefaultNodeShape000
setDefaultNodeSize000
setDefaultNodeWidth000
setDefaultStyle000
setEdgeStyle000
setGraph000
setNodeAttributes000
setNodeBorderColor000
setNodeBorderWidth000
setNodeColor000
setNodeColorRule000
setNodeFontColor000
setNodeFontSize000
setNodeHeight000
setNodeLabelRule000
setNodeShape000
setNodeSize000
setNodeSizeRule000
setNodeWidth000
setPosition000
setZoom000
sfn000
showAll000
showEdges000
simpleDemoGraph0.040.000.05
vAlign000