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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:rrvgo.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings rrvgo_1.0.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/rrvgo.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'rrvgo/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'rrvgo' version '1.0.2'
* package encoding: UTF-8
* 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 'rrvgo' 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 ... NOTE
Unexported object imported by a ':::' call: 'GOSemSim:::getAncestors'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
scatterPlot: no visible binding for global variable 'V1'
scatterPlot: no visible binding for global variable 'V2'
scatterPlot: no visible binding for global variable 'parentTerm'
scatterPlot: no visible binding for global variable 'parent'
Undefined global functions or variables:
  V1 V2 parent parentTerm
* 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
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
wordcloudPlot      121.43   0.39  121.85
treemapPlot        116.57   0.34  116.92
reduceSimMatrix    107.00   0.35  107.39
scatterPlot        106.97   0.34  107.45
heatmapPlot        105.56   0.56  106.13
calculateSimMatrix 101.12   0.41  108.37
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
treemapPlot        62.89   0.24   63.17
scatterPlot        53.67   0.34   54.07
reduceSimMatrix    50.05   0.50   50.57
wordcloudPlot      47.63   0.34   47.99
heatmapPlot        46.64   0.47   47.15
calculateSimMatrix 42.34   0.33   42.69
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/rrvgo.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/rrvgo_1.0.2.tar.gz && rm -rf rrvgo.buildbin-libdir && mkdir rrvgo.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=rrvgo.buildbin-libdir rrvgo_1.0.2.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL rrvgo_1.0.2.zip && rm rrvgo_1.0.2.tar.gz rrvgo_1.0.2.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  216k  100  216k    0     0  3395k      0 --:--:-- --:--:-- --:--:-- 3792k

install for i386

* installing *source* package 'rrvgo' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'rrvgo'
    finding HTML links ... done
    calculateSimMatrix                      html  
    getGoSize                               html  
    getGoTerm                               html  
    gg_color_hue                            html  
    heatmapPlot                             html  
    loadOrgdb                               html  
    reduceSimMatrix                         html  
    scatterPlot                             html  
    shiny_rrvgo                             html  
    treemapPlot                             html  
    wordcloudPlot                           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 'rrvgo' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'rrvgo' as rrvgo_1.0.2.zip
* DONE (rrvgo)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'rrvgo' successfully unpacked and MD5 sums checked