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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:XINA.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings XINA_1.10.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/XINA.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'XINA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'XINA' version '1.10.0'
* 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 'XINA' 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
xina_clustering             50.25   0.09   50.34
plot_condition_compositions 13.52   0.00   13.52
mutate_colors                8.81   0.06    8.88
plot_clusters                8.19   0.06    8.25
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                   user system elapsed
xina_clustering                   46.03   0.03   46.08
plot_condition_compositions       13.13   0.00   13.13
plot_clusters                      8.31   0.03    8.34
mutate_colors                      7.94   0.00    7.94
get_condition_biased_comigrations  5.20   0.03    5.23
* 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://155.52.207.165/BBS/3.13/bioc/src/contrib/XINA_1.10.0.tar.gz && rm -rf XINA.buildbin-libdir && mkdir XINA.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=XINA.buildbin-libdir XINA_1.10.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL XINA_1.10.0.zip && rm XINA_1.10.0.tar.gz XINA_1.10.0.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  643k  100  643k    0     0  1543k      0 --:--:-- --:--:-- --:--:-- 1546k

install for i386

* installing *source* package 'XINA' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'XINA'
    finding HTML links ... done
    add_legend                              html  
    alluvial_enriched                       html  
    alluvial_enrichment_tests               html  
    calculate_centrality_scores             html  
    default_size                            html  
    draw_alluvial_plot                      html  
    example_clusters                        html  
    extract_data_column                     html  
    find_similar_clusters                   html  
    generate_count_table                    html  
    generate_superset                       html  
    get_color_for_nodes                     html  
    get_colors                              html  
    get_comigrations_by_name                html  
    get_condition_biased_comigrations       html  
    get_layout                              html  
    get_mTOR_proteins                       html  
    get_random_data                         html  
    get_stats                               html  
    get_theme_blank                         html  
    get_unknown_ppi_nodes                   html  
    gn                                      html  
    gn_desc                                 html  
    hprd_ppi                                html  
    length2                                 html  
    load_previous_results                   html  
    make_random_xina_data                   html  
    mutate_colors                           html  
    organize_clusters                       html  
    plot_NA                                 html  
    plot_clusters                           html  
    plot_clusters_all                       html  
    plot_condition_compositions             html  
    plot_enrichment_results                 html  
    rank_centrality                         html  
    string_example                          html  
    xina_analysis                           html  
    xina_clustering                         html  
    xina_enrichment                         html  
    xina_plot_all                           html  
    xina_plot_bycluster                     html  
    xina_plot_single                        html  
    xina_result_example                     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 'XINA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'XINA' as XINA_1.10.0.zip
* DONE (XINA)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'XINA' successfully unpacked and MD5 sums checked