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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CIMICE.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings CIMICE_1.3.1.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/CIMICE.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CIMICE/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CIMICE' version '1.3.1'
* 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 ... NOTE
Found the following hidden files and directories:
  .git.bfg-report
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'CIMICE' 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
* 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 files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  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: 1 NOTE
See
  'D:/biocbuild/bbs-3.15-bioc/meat/CIMICE.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL CIMICE
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'CIMICE' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'CIMICE'
    finding HTML links ... done
    CIMICE                                  html  
    annotate_mutational_matrix              html  
    binary_radix_sort                       html  
    build_subset_graph                      html  
    build_topology_subset                   html  
    chunk_reader                            html  
    compact_dataset                         html  
    computeDWNW                             html  
    computeDWNW_aux                         html  
    computeUPW                              html  
    computeUPW_aux                          html  
    compute_weights_default                 html  
    corrplot_from_mutational_matrix         html  
    corrplot_genes                          html  
    corrplot_samples                        html  
    dataset_preprocessing                   html  
    dataset_preprocessing_population        html  
    draw_ggraph                             html  
    draw_networkD3                          html  
    draw_visNetwork                         html  
    example_dataset                         html  
    example_dataset_withFreqs               html  
    finalize_generator                      html  
    fix_clonal_genotype                     html  
    format_labels                           html  
    gene_mutations_hist                     html  
    get_no_of_children                      html  
    graph_non_transitive_subset_topology    html  
    make_dataset                            html  
    make_generator_stub                     html  
    make_labels                             html  
    normalizeDWNW                           html  
    normalizeUPW                            html  
    perturb_dataset                         html  
    plot_generator                          html  
    prepare_generator_edge_set_command      html  
    prepare_labels                          html  
    quick_run                               html  
    read                                    html  
    read_CAPRI                              html  
    read_CAPRI_string                       html  
    read_CAPRIpop                           html  
    read_CAPRIpop_string                    html  
    read_MAF                                html  
    read_matrix                             html  
    remove_transitive_edges                 html  
    sample_mutations_hist                   html  
    select_genes_on_mutations               html  
    select_samples_on_mutations             html  
    set_generator_edges                     html  
    simulate_generator                      html  
    to_dot                                  html  
    update_df                               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
* DONE (CIMICE)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'iBBiG' is missing or broken
 done

R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(CIMICE)
> 
> test_check("CIMICE")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
> 
> proc.time()
   user  system elapsed 
   2.14    0.23    2.35