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INSTALL report for BiocOncoTK on tokay1

This page was generated on 2020-08-06 12:07:26 -0400 (Thu, 06 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE BiocOncoTK PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 155/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocOncoTK 1.9.0
VJ Carey
Snapshot Date: 2020-08-05 14:50:59 -0400 (Wed, 05 Aug 2020)
URL: https://git.bioconductor.org/packages/BiocOncoTK
Branch: master
Last Commit: e08ae5b
Last Changed Date: 2020-04-27 15:16:30 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64 [ OK ] OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BiocOncoTK
Version: 1.9.0
Command: C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/BiocOncoTK_1.9.0.tar.gz && rm -rf BiocOncoTK.buildbin-libdir && mkdir BiocOncoTK.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BiocOncoTK.buildbin-libdir BiocOncoTK_1.9.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL BiocOncoTK_1.9.0.zip && rm BiocOncoTK_1.9.0.tar.gz BiocOncoTK_1.9.0.zip
StartedAt: 2020-08-05 18:46:10 -0400 (Wed, 05 Aug 2020)
EndedAt: 2020-08-05 18:47:36 -0400 (Wed, 05 Aug 2020)
EllapsedTime: 86.0 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/BiocOncoTK_1.9.0.tar.gz && rm -rf BiocOncoTK.buildbin-libdir && mkdir BiocOncoTK.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BiocOncoTK.buildbin-libdir BiocOncoTK_1.9.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL BiocOncoTK_1.9.0.zip && rm BiocOncoTK_1.9.0.tar.gz BiocOncoTK_1.9.0.zip
###
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100 7803k  100 7803k    0     0  48.7M      0 --:--:-- --:--:-- --:--:-- 49.8M

install for i386

Warning in untar2(tarfile, files, list, exdir, restore_times) :
  failed to copy 'BiocOncoTK/vignettes/BiocOncoTK.Rmd' to 'BiocOncoTK/README.md'
* installing *source* package 'BiocOncoTK' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'BiocOncoTK'
    finding HTML links ... done
    CCLE_DRUG_BROAD                         html  
    MSIsensor.10k                           html  
    TcgaMutCounts                           html  
    TcgaNIndWithAnyMut                      html  
    add_sym                                 html  
    annotTabs                               html  
    bindMSI                                 html  
    bipg_tests                              html  
    brcaMAE                                 html  
    buildPancanSE                           html  
    cell_70138                              html  
    clueDemos                               html  
    clueServiceNames                        html  
    darmGBMcls                              html  
    dingMSI                                 html  
    featIDMapper                            html  
    fireMSI                                 html  
    get_plates                              html  
    ggFeatDens                              html  
    ggFeatureSegs                           html  
    ggMutDens                               html  
    icd10_c                                 html  
    k23sig                                  html  
    kang_DNArepair                          html  
    loadPatel                               html  
    log10pl1                                html  
    map_tcga_ncit                           html  
    mc3toGR                                 html  
    molpo_3utr                              html  
    molpo_5utr                              html  
    molpo_CDS                               html  
    molpo_WGS                               html  
    multiviz                                html  
    oncoPrintISB                            html  
    pancan.clin.varnames                    html  
    pancan_BQ                               html  
    finding level-2 HTML links ... done

    pancan_app                              html  
    pancan_clinicalTabVarnames              html  
    pancan_longname                         html  
    pancan_sampTypeMap                      html  
    pancan_tabulate                         html  
    patient_to_tumor_code                   html  
    pertClasses                             html  
    pert_70138                              html  
    query_clue                              html  
    reexports                               html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpiIfakE/R.INSTALL2b3815e16b70/BiocOncoTK/man/reexports.Rd:19: file link '%>%' in package 'magrittr' does not exist and so has been treated as a topic
    replaceRownames                         html  
    small_msi                               html  
    tumNorSet                               html  
    utils                                   html  
    viz_msi_raw                             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 'BiocOncoTK/vignettes/BiocOncoTK.Rmd' to 'BiocOncoTK/README.md'
* installing *source* package 'BiocOncoTK' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BiocOncoTK' as BiocOncoTK_1.9.0.zip
* DONE (BiocOncoTK)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'BiocOncoTK' successfully unpacked and MD5 sums checked