Package: RCy3

Version: 2.4.6

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RCy3.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings RCy3_2.4.6.tar.gz

StartedAt: 2019-10-16 06:23:36 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 06:25:04 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 88.4 seconds

RetCode: 0

Status:  OK

CheckDir: RCy3.Rcheck

Warnings: 0

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RCy3.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings RCy3_2.4.6.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/RCy3.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RCy3/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RCy3' version '2.4.6'
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'RCy3' 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 ... NOTE
createNetworkFromDataFrames: no visible binding for global variable
  'SUID'
Undefined global functions or variables:
  SUID
* 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 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/RCy3.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/RCy3_2.4.6.tar.gz && rm -rf RCy3.buildbin-libdir && mkdir RCy3.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RCy3.buildbin-libdir RCy3_2.4.6.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL RCy3_2.4.6.zip && rm RCy3_2.4.6.tar.gz RCy3_2.4.6.zip
###
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  % 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  700k  100  700k    0     0  11.2M      0 --:--:-- --:--:-- --:--:-- 12.6M

install for i386

* installing *source* package 'RCy3' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'RCy3'
    finding HTML links ... done
    AddToGroup                              html  
    RCy3                                    html  
    RemoveFromGroup                         html  
    addCyEdges                              html  
    addCyNodes                              html  
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    bundleEdges                             html  
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    commandOpenDialog                       html  
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    commandsGET                             html  
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    createCompositeFilter                   html  
    createDegreeFilter                      html  
    createGraphFromNetwork                  html  
    createGroup                             html  
    createIgraphFromNetwork                 html  
    createNetworkFromDataFrames             html  
    createNetworkFromGraph                  html  
    createNetworkFromIgraph                 html  
    createSubnetwork                        html  
    createVisualStyle                       html  
    cybrowserClose                          html  
    cybrowserDialog                         html  
    cybrowserHide                           html  
    cybrowserList                           html  
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    getNetworkSuid                          html  
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    getNetworkViews                         html  
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    getTableValue                           html  
    getUninstalledApps                      html  
    getVisualPropertyDefault                html  
    getVisualPropertyNames                  html  
    getVisualStyleNames                     html  
    hideAllPanels                           html  
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    hideNodes                               html  
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    selectEdgesAdjacentToSelectedNodes      html  
    selectEdgesConnectingSelectedNodes      html  
    selectFirstNeighbors                    html  
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    updateNetworkInNDEx                     html  
    updateStyleDefaults                     html  
    updateStyleMapping                      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 'RCy3' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RCy3' as RCy3_2.4.6.zip
* DONE (RCy3)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'RCy3' successfully unpacked and MD5 sums checked

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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.

> # tests disabled as the Bioconductor build system no longer supports interactive sessions
> #require(RCy3) || stop("unable to load RCy3")
> #BiocGenerics:::testPackage('RCy3')
> 
> proc.time()
   user  system elapsed 
   0.29    0.01    0.28 

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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.

> # tests disabled as the Bioconductor build system no longer supports interactive sessions
> #require(RCy3) || stop("unable to load RCy3")
> #BiocGenerics:::testPackage('RCy3')
> 
> proc.time()
   user  system elapsed 
   0.21    0.06    0.26