Package: TCGAutils

Version: 1.3.33

Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/TCGAutils_1.3.33.tar.gz && rm -rf TCGAutils.buildbin-libdir && mkdir TCGAutils.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TCGAutils.buildbin-libdir TCGAutils_1.3.33.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL TCGAutils_1.3.33.zip && rm TCGAutils_1.3.33.tar.gz TCGAutils_1.3.33.zip

StartedAt: 2019-04-08 20:04:43 -0400 (Mon, 08 Apr 2019)

EndedAt: 2019-04-08 20:05:49 -0400 (Mon, 08 Apr 2019)

EllapsedTime: 66.4 seconds

RetCode: 0

Status:  OK

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### Running command:
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###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/TCGAutils_1.3.33.tar.gz && rm -rf TCGAutils.buildbin-libdir && mkdir TCGAutils.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TCGAutils.buildbin-libdir TCGAutils_1.3.33.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL TCGAutils_1.3.33.zip && rm TCGAutils_1.3.33.tar.gz TCGAutils_1.3.33.zip
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install for i386

Warning in untar2(tarfile, files, list, exdir, restore_times) :
  failed to copy 'TCGAutils/inst/NEWS' to 'TCGAutils/NEWS.md'
* installing *source* package 'TCGAutils' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'TCGAutils'
    finding HTML links ... done
    ID-translation                          html  
    TCGAbarcode                             html  
    TCGAbiospec                             html  
    TCGAsampleSelect                        html  
    finding level-2 HTML links ... done

    TCGAutils-package                       html  
    builds                                  html  
    clinicalNames                           html  
    curatedTCGAData-helpers                 html  
    diseaseCodes                            html  
    findGRangesCols                         html  
    generateMap                             html  
    getFileName                             html  
    hidden-helpers                          html  
    imputeAssay                             html  
    makeGRangesListFromCopyNumber           html  
    makeGRangesListFromExonFiles            html  
    makeSummarizedExperimentFromGISTIC      html  
    mergeColData                            html  
    sampleTypes                             html  
    simplifyTCGA                            html  
    trimColData                             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

Warning in untar2(tarfile, files, list, exdir, restore_times) :
  failed to copy 'TCGAutils/inst/NEWS' to 'TCGAutils/NEWS.md'
* installing *source* package 'TCGAutils' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'TCGAutils' as TCGAutils_1.3.33.zip
* DONE (TCGAutils)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'TCGAutils' successfully unpacked and MD5 sums checked