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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Chicago.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings Chicago_1.22.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/Chicago.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 'Chicago/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Chicago' version '1.22.0'
* 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 'Chicago' 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 ... OK
* 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
normaliseOtherEnds 19.82   3.89   23.78
exportResults      14.96   1.19   16.14
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
normaliseOtherEnds 17.72   3.76   19.71
exportResults      12.49   0.49   12.97
* 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: OK

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/Chicago_1.22.0.tar.gz && rm -rf Chicago.buildbin-libdir && mkdir Chicago.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Chicago.buildbin-libdir Chicago_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL Chicago_1.22.0.zip && rm Chicago_1.22.0.tar.gz Chicago_1.22.0.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
 78  433k   78  341k    0     0   534k      0 --:--:-- --:--:-- --:--:--  534k
100  433k  100  433k    0     0   607k      0 --:--:-- --:--:-- --:--:--  607k

install for i386

* installing *source* package 'Chicago' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'Chicago'
    finding HTML links ... done
    Chicago-package                         html  
    cdUnitTest                              html  
    chicagoData                             html  
    chicagoPipeline                         html  
    copyCD                                  html  
    defaultSettings                         html  
    estimateBrownianComponent               html  
    estimateDistFun                         html  
    estimateTechnicalNoise                  html  
    exportResults                           html  
    getPvals                                html  
    getScores                               html  
    getSkOnly                               html  
    mergeSamples                            html  
    modifySettings                          html  
    normaliseBaits                          html  
    normaliseOtherEnds                      html  
    overlapFragWithFeatures                 html  
    finding level-2 HTML links ... done

    peakEnrichment4Features                 html  
    plotBaits                               html  
    plotDistFun                             html  
    readAndMerge                            html  
    readSample                              html  
    setExperiment                           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 'Chicago' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Chicago' as Chicago_1.22.0.zip
* DONE (Chicago)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'Chicago' successfully unpacked and MD5 sums checked