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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:deltaCaptureC.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings deltaCaptureC_1.4.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/deltaCaptureC.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'deltaCaptureC/DESCRIPTION' ... OK
* this is package 'deltaCaptureC' 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 'deltaCaptureC' 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
getDeltaSE: warning in SummarizedExperiment(assay = list(delta =
  delta), colData = colData): partial argument match of 'assay' to
  'assays'
plotSignificantRegions: no visible binding for global variable 'ctr'
plotSignificantRegions: no visible binding for global variable 'delta'
plotSignificantRegions: no visible binding for global variable
  'significance'
Undefined global functions or variables:
  ctr delta significance
* 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
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
binSummarizedExperiment 147.11   0.23  148.89
getOverlapWeights        20.71   0.00   26.55
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
binSummarizedExperiment 159.25   0.06  159.55
getOverlapWeights        16.08   0.01   16.10
* 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 NOTE
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/deltaCaptureC.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/deltaCaptureC_1.4.0.tar.gz && rm -rf deltaCaptureC.buildbin-libdir && mkdir deltaCaptureC.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=deltaCaptureC.buildbin-libdir deltaCaptureC_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL deltaCaptureC_1.4.0.zip && rm deltaCaptureC_1.4.0.tar.gz deltaCaptureC_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
100  371k  100  371k    0     0  24.9M      0 --:--:-- --:--:-- --:--:-- 27.8M

install for i386

* installing *source* package 'deltaCaptureC' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'deltaCaptureC'
    finding HTML links ... done
    bigBinSize                              html  
    binSummarizedExperiment                 html  
    binnedDeltaPlot                         html  
    binnedDeltaSE                           html  
    binnedSummarizedExperiment              html  
    deltaSE                                 html  
    dot-getRunsAndTotals                    html  
    downshiftDFtoMatrix                     html  
    generatePermutation                     html  
    getDeltaSE                              html  
    getLopsidedness                         html  
    getMeanNormalizedCountsSE               html  
    getNormalizedCountsSE                   html  
    getOverlapWeights                       html  
    getPValueCutoff                         html  
    getRunAndLopsidednessStatistics         html  
    getRunStatistics                        html  
    getRunStatisticsDist                    html  
    getRunTotals                            html  
    getSignificantRegions                   html  
    getSizeFactorsDF                        html  
    getSizeFactorsSE                        html  
    miniDeltaSE                             html  
    miniSE                                  html  
    miniSEDF                                html  
    numPermutations                         html  
    pValue                                  html  
    plotSignificantRegions                  html  
    plotTitle                               html  
    rebinToMultiple                         html  
    regionOfInterest                        html  
    significanceType                        html  
    significantRegions                      html  
    significantRegionsPlot                  html  
    smallBinSize                            html  
    smallBins                               html  
    smallSetOfSmallBins                     html  
    smallerDeltaSE                          html  
    viewpointRegion                         html  
    weightsExampleBins                      html  
    weightsExampleGr                        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 'deltaCaptureC' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'deltaCaptureC' as deltaCaptureC_1.4.0.zip
* DONE (deltaCaptureC)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'deltaCaptureC' successfully unpacked and MD5 sums checked