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### Running command:
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###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:optimalFlow.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings optimalFlow_1.7.0.tar.gz
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/optimalFlow.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'optimalFlow/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'optimalFlow' version '1.7.0'
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'optimalFlow' 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
* 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
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'GaussianBarycenters' 'distGaussianCov' 'distGaussianMean'
  'wassersteinKBarycenter'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
voteLabelTransfer: no visible binding for global variable 'cell'
voteLabelTransfer: no visible binding for global variable
  'compound.proportion'
voteLabelTransfer: no visible binding for global variable
  'vote.proportion'
voteTransformation : <anonymous>: no visible binding for global
  variable 'cell'
voteTransformation : <anonymous>: no visible binding for global
  variable 'simple.proportion'
voteTransformation : <anonymous>: no visible binding for global
  variable 'compound.proportion'
Undefined global functions or variables:
  cell compound.proportion simple.proportion vote.proportion
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
cytoPlot                  1.83   0.25   27.47
wasserCostFunction        0.85   0.16   28.07
f1ScoreVoting             0.69   0.20   49.95
cytoPlotDatabase          0.70   0.09   24.61
optimalFlowClassification 0.58   0.19   47.69
cytoPlot3d                0.36   0.09   26.14
optimalFlowTemplates      0.27   0.15   38.36
cytoPlotDatabase3d        0.27   0.13   43.69
* 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:/biocbuild/bbs-3.15-bioc/meat/optimalFlow.Rcheck/00check.log'
for details.

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### Running command:
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###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL optimalFlow
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'optimalFlow' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'optimalFlow'
    finding HTML links ... done
    costWasserMatchingEllipse               html  
    cytoPlot                                html  
    cytoPlot3d                              html  
    cytoPlotDatabase                        html  
    cytoPlotDatabase3d                      html  
    estimCovCellGeneral                     html  
    estimationCellBarycenter                html  
    f1Score                                 html  
    f1ScoreVoting                           html  
    labelTransfer                           html  
    labelTransferEllipse                    html  
    optimalFlowClassification               html  
    optimalFlowTemplates                    html  
    qdaClassification                       html  
    tclustWithInitialization                html  
    tclust_H                                html  
    trimmedKBarycenter                      html  
    voteLabelTransfer                       html  
    w2dist                                  html  
    wasserCostFunction                      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
* DONE (optimalFlow)
Making 'packages.html' ... done