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This page was generated on 2021-06-18 12:05:05 -0400 (Fri, 18 Jun 2021).

CHECK results for RCyjs on riesling1

To the developers/maintainers of the RCyjs package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RCyjs.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1490/1993HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RCyjs 2.15.0  (landing page)
Paul Shannon
Snapshot Date: 2021-06-17 14:50:06 -0400 (Thu, 17 Jun 2021)
URL: https://git.bioconductor.org/packages/RCyjs
Branch: master
Last Commit: 31dd51d
Last Changed Date: 2021-05-19 12:13:00 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: RCyjs
Version: 2.15.0
Command: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RCyjs.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings RCyjs_2.15.0.tar.gz
StartedAt: 2021-06-18 01:49:06 -0400 (Fri, 18 Jun 2021)
EndedAt: 2021-06-18 01:53:03 -0400 (Fri, 18 Jun 2021)
EllapsedTime: 236.8 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: RCyjs.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RCyjs.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings RCyjs_2.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.14-bioc/meat/RCyjs.Rcheck'
* using R version 4.1.0 (2021-05-18)
* 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 '2.15.0'
* 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 'RCyjs' can be installed ... 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
* 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 ... WARNING
Undocumented arguments in documentation object 'hideNodes,RCyjs-method'
  'nodeIDs'

Undocumented arguments in documentation object 'readAndStandardizeJSONNetworkFile'
  'filename'
Documented arguments not in \usage in documentation object 'readAndStandardizeJSONNetworkFile':
  'file'

Undocumented arguments in documentation object 'readAndStandardizeJSONStyleFile'
  'filename'
Documented arguments not in \usage in documentation object 'readAndStandardizeJSONStyleFile':
  'file'

Undocumented arguments in documentation object 'showNodes,RCyjs-method'
  'nodeIDs'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking include directives in Makefiles ... 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' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING
See
  'D:/biocbuild/bbs-3.14-bioc/meat/RCyjs.Rcheck/00check.log'
for details.



Installation output

RCyjs.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/RCyjs_2.15.0.tar.gz && rm -rf RCyjs.buildbin-libdir && mkdir RCyjs.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RCyjs.buildbin-libdir RCyjs_2.15.0.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL RCyjs_2.15.0.zip && rm RCyjs_2.15.0.tar.gz RCyjs_2.15.0.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  892k  100  892k    0     0  4461k      0 --:--:-- --:--:-- --:--:-- 4461k

install for i386

* installing *source* package 'RCyjs' ...
** using staged installation
** 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  
    dataFramesToJSON                        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  
    graphNELtoJSON.string                   html  
    hAlign                                  html  
    hideAllEdges                            html  
    hideEdges                               html  
    hideNodes                               html  
    hideSelectedNodes                       html  
    invertNodeSelection                     html  
    layout                                  html  
    layoutSelectionInGrid                   html  
    layoutSelectionInGridInferAnchorm       html  
    loadStyleFile                           html  
    noa                                     html  
    noaNames                                html  
    readAndStandardizeJSONNetworkFile       html  
    readAndStandardizeJSONStyleFile         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  
    showNodes                               html  
    simpleDemoGraph                         html  
    vAlign                                  html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'RCyjs' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RCyjs' as RCyjs_2.15.0.zip
* DONE (RCyjs)
* installing to library 'D:/biocbuild/bbs-3.14-bioc/R/library'
package 'RCyjs' successfully unpacked and MD5 sums checked

Tests output

RCyjs.Rcheck/tests_i386/runTests.Rout


R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
Copyright (C) 2021 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 
   0.10    0.01    0.10 

RCyjs.Rcheck/tests_x64/runTests.Rout


R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
Copyright (C) 2021 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 
   0.10    0.03    0.12 

Example timings

RCyjs.Rcheck/examples_i386/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
graphNELtoJSON.string000
hAlign000
hideAllEdges000
hideEdges000
hideNodes000
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
setNodeLabelRule0.020.000.02
setNodeShape000
setNodeSize000
setNodeSizeRule000
setNodeWidth000
setPosition000
setZoom000
sfn000
showAll000
showEdges000
showNodes000
simpleDemoGraph0.030.000.03
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
graphNELtoJSON.string000
hAlign000
hideAllEdges000
hideEdges000
hideNodes000
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
setDefaultNodeFontColor0.020.000.02
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
showNodes000
simpleDemoGraph0.030.000.03
vAlign000