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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:epigenomix.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings epigenomix_1.30.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/epigenomix.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 'epigenomix/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'epigenomix' version '1.30.0'
* 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 'epigenomix' 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
plotChains    34.27   0.00   34.26
bayesMixModel 27.33   0.25   27.58
mlMixModel    12.94   0.16   13.10
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
plotChains    30.08   0.01   30.09
bayesMixModel 27.94   0.01   27.95
mlMixModel    13.85   0.07   13.93
* 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://172.29.0.3/BBS/3.12/bioc/src/contrib/epigenomix_1.30.0.tar.gz && rm -rf epigenomix.buildbin-libdir && mkdir epigenomix.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=epigenomix.buildbin-libdir epigenomix_1.30.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL epigenomix_1.30.0.zip && rm epigenomix_1.30.0.tar.gz epigenomix_1.30.0.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  212k  100  212k    0     0  12.9M      0 --:--:-- --:--:-- --:--:-- 13.8M

install for i386

* installing *source* package 'epigenomix' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning in .recacheSubclasses(def@className, def, env) :
  undefined subclass "numericVector" of class "Mnumeric"; definition not updated
** help
*** installing help indices
  converting help for package 'epigenomix'
    finding HTML links ... done
    ChIPseqSet-class                        html  
    finding level-2 HTML links ... done

    MixModel-class                          html  
    MixModelBayes-class                     html  
    MixModelML-class                        html  
    MixtureComponent-class                  html  
    bayesMixModel                           html  
    calculateCrossCorrelation               html  
    eSet                                    html  
    fpkm                                    html  
    getAlignmentQuality                     html  
    integrateData                           html  
    mappedReads                             html  
    matchProbeToPromoter                    html  
    mlMixModel                              html  
    normalize                               html  
    normalizeChIP                           html  
    plotChains                              html  
    plotClassification                      html  
    plotComponents                          html  
    summarizeReads                          html  
    transToTSS                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning in .recacheSubclasses(def@className, def, env) :
  undefined subclass "numericVector" of class "Mnumeric"; definition not updated
** testing if installed package can be loaded from final location
Warning in .recacheSubclasses(def@className, def, env) :
  undefined subclass "numericVector" of class "Mnumeric"; definition not updated
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'epigenomix' ...
** testing if installed package can be loaded
Warning in .recacheSubclasses(def@className, def, env) :
  undefined subclass "numericVector" of class "Mnumeric"; definition not updated
* MD5 sums
packaged installation of 'epigenomix' as epigenomix_1.30.0.zip
* DONE (epigenomix)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'epigenomix' successfully unpacked and MD5 sums checked