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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pipeComp.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings pipeComp_1.4.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/pipeComp.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'pipeComp/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'pipeComp' version '1.4.0'
* 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 'pipeComp' 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 ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  '.compileExcludedCells' '.getMM' '.homogenizeDEA' '.runf'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
scrna_describeDatasets: no visible binding for global variable
  'cluster'
scrna_describeDatasets: no visible binding for global variable 'nb'
scrna_describeDatasets : pf: no visible binding for global variable
  '.x'
scrna_describeDatasets : rd: no visible binding for global variable 'y'
scrna_describeDatasets : rd: no visible binding for global variable
  'cluster'
scrna_evalPlot_filtering: no visible binding for global variable
  'max.lost'
scrna_evalPlot_filtering: no visible binding for global variable
  'mean_F1'
scrna_evalPlot_filtering: no visible binding for global variable 'filt'
scrna_evalPlot_filtering: no visible binding for global variable
  'doubletmethod'
scrna_evalPlot_filtering: no visible binding for global variable
  'method'
scrna_evalPlot_overall: no visible binding for global variable
  'true.nbClusts'
scrna_evalPlot_overall: no visible binding for global variable 'n_clus'
Undefined global functions or variables:
  .x cluster doubletmethod filt max.lost mean_F1 method n_clus nb
  true.nbClusts y
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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 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-3.14-bioc/meat/pipeComp.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/pipeComp_1.4.0.tar.gz && rm -rf pipeComp.buildbin-libdir && mkdir pipeComp.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=pipeComp.buildbin-libdir pipeComp_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL pipeComp_1.4.0.zip && rm pipeComp_1.4.0.tar.gz pipeComp_1.4.0.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
  0 1051k    0  2487    0     0  30316      0  0:00:35 --:--:--  0:00:35 30329
100 1051k  100 1051k    0     0  1322k      0 --:--:-- --:--:-- --:--:-- 1321k

install for i386

* installing *source* package 'pipeComp' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'pipeComp'
    finding HTML links ... done
    PipelineDefinition-methods              html  
    PipelineDefinition                      html  
    addPipelineStep                         html  
    aggregatePipelineResults                html  
    buildCombMatrix                         html  
    checkPipelinePackages                   html  
    clustMetricsCorr                        html  
    colCenterScale                          html  
    ctrlgenes                               html  
    dea_evalPlot_curve                      html  
    dea_pipeline                            html  
    defaultStepAggregation                  html  
    evalHeatmap                             html  
    evaluateClustering                      html  
    evaluateDEA                             html  
    evaluateDimRed                          html  
    evaluateNorm                            html  
    exampleDEAresults                       html  
    exampleResults                          html  
    farthestPoint                           html  
    getDimensionality                       html  
    getQualitativePalette                   html  
    match_evaluate_multiple                 html  
    mergePipelineResults                    html  
    mockPipeline                            html  
    parsePipNames                           html  
    pipeComp-package                        html  
    plotElapsed                             html  
    readPipelineResults                     html  
    runPipeline                             html  
    scrna_describeDatasets                  html  
    scrna_evalPlot_filtering                html  
    scrna_evalPlot_overall                  html  
    scrna_evalPlot_silh                     html  
    scrna_pipeline                          html  
    stableG                                 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 'pipeComp' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'pipeComp' as pipeComp_1.4.0.zip
* DONE (pipeComp)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'pipeComp' successfully unpacked and MD5 sums checked