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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:YAPSA.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings YAPSA_1.20.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/YAPSA.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'YAPSA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'YAPSA' version '1.20.1'
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'YAPSA' 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 ... NOTE
read_list: no visible global function definition for 'detectCores'
read_list: no visible global function definition for 'makeCluster'
read_list: no visible global function definition for 'mclapply'
read_list: no visible global function definition for 'stopCluster'
Undefined global functions or variables:
  detectCores makeCluster mclapply stopCluster
* 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 installed files from 'inst/doc' ... 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
confidence_indel_only_calulation        23.75   0.33   24.07
create_indel_mutation_catalogue_from_df 15.63   0.62   16.27
build_gene_list_for_pathway              8.11   0.19   27.31
run_SMC                                  5.68   0.50    6.19
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                         user system elapsed
confidence_indel_only_calulation        22.26   0.07   22.33
create_indel_mutation_catalogue_from_df 14.41   0.57   14.97
build_gene_list_for_pathway              8.34   0.04   27.36
run_SMC                                  5.44   0.44    5.87
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/YAPSA.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/YAPSA_1.20.1.tar.gz && rm -rf YAPSA.buildbin-libdir && mkdir YAPSA.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=YAPSA.buildbin-libdir YAPSA_1.20.1.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL YAPSA_1.20.1.zip && rm YAPSA_1.20.1.tar.gz YAPSA_1.20.1.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
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 23 1293k   23  306k    0     0   630k      0  0:00:02 --:--:--  0:00:02  631k
100 1293k  100 1293k    0     0  1053k      0  0:00:01  0:00:01 --:--:-- 1054k

install for i386

* installing *source* package 'YAPSA' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
** help
*** installing help indices
  converting help for package 'YAPSA'
    finding HTML links ... done
    GenomeOfNl_raw                          html  
    LCD                                     html  
    LCD_SMC                                 html  
    LCD_complex_cutoff                      html  
    MutCat_indel_df                         html  
    SMC                                     html  
    SMC_perPID                              html  
    YAPSA                                   html  
    add_annotation                          html  
    add_as_fist_to_list                     html  
    aggregate_exposures_by_category         html  
    annotate_intermut_dist_PID              html  
    annotate_intermut_dist_cohort           html  
    annotation_exposures_barplot            html  
    annotation_exposures_list_barplot       html  
    annotation_heatmap_exposures            html  
    attribute_nucleotide_exchanges          html  
    attribute_sequence_contex_indel         html  
    attribution_of_indels                   html  
    build_gene_list_for_pathway             html  
    classify_indels                         html  
    compare_SMCs                            html  
    compare_exposures                       html  
    compare_expousre_sets                   html  
    compare_sets                            html  
    compare_to_catalogues                   html  
    complex_heatmap_exposures               html  
    computeLogLik                           html  
    compute_comparison_stat_df              html  
    confIntExp                              html  
    confidence_indel_calulation             html  
    confidence_indel_only_calulation        html  
    correct_rounded                         html  
    cosineDist                              html  
    cosineMatchDist                         html  
    create_indel_mut_cat_from_df            html  
    create_indel_mutation_catalogue_from_df
                                            html  
    create_mutation_catalogue_from_VR       html  
    create_mutation_catalogue_from_df       html  
    finding level-2 HTML links ... done

    cut_breaks_as_intervals                 html  
    cutoffs                                 html  
    cutoffs_pcawg                           html  
    deriveSigInd_df                         html  
    disambiguateVector                      html  
    enrichSigs                              html  
    exampleINDEL_YAPSA                      html  
    exampleYAPSA                            html  
    exchange_colour_vector                  html  
    exome_mutCatRaw_df                      html  
    exposures_barplot                       html  
    extract_names_from_gene_list            html  
    find_affected_PIDs                      html  
    getSequenceContext                      html  
    get_extreme_PIDs                        html  
    hclust_exposures                        html  
    logLikelihood                           html  
    lymphomaNature2013_mutCat_df            html  
    makeVRangesFromDataFrame                html  
    make_catalogue_strata_df                html  
    make_comparison_matrix                  html  
    make_strata_df                          html  
    make_subgroups_df                       html  
    melt_exposures                          html  
    merge_exposures                         html  
    normalizeMotifs_otherRownames           html  
    normalize_df_per_dim                    html  
    plotExchangeSpectra                     html  
    plotExchangeSpectra_indel               html  
    plotExposuresConfidence                 html  
    plotExposuresConfidence_indel           html  
    plot_SMC                                html  
    plot_exposures                          html  
    plot_strata                             html  
    read_entry                              html  
    relateSigs                              html  
    repeat_df                               html  
    round_precision                         html  
    run_SMC                                 html  
    run_annotate_vcf_pl                     html  
    run_comparison_catalogues               html  
    run_comparison_general                  html  
    run_kmer_frequency_correction           html  
    run_kmer_frequency_normalization        html  
    run_plot_strata_general                 html  
    shapiro_if_possible                     html  
    sigs                                    html  
    sigs_pcawg                              html  
    split_exposures_by_subgroups            html  
    stat_plot_subgroups                     html  
    stat_test_SMC                           html  
    stat_test_subgroups                     html  
    stderrmean                              html  
    sum_over_list_of_df                     html  
    targetCapture_cor_factors               html  
    temp_trellis_rainfall_plot              html  
    testSigs                                html  
    test_exposureAffected                   html  
    test_gene_list_in_exposures             html  
    transform_rownames_R_to_MATLAB          html  
    translate_to_hg19                       html  
    trellis_rainfall_plot                   html  
    trellis_rainfall_plot_old               html  
    variateExp                              html  
    variateExpSingle                        html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
** testing if installed package can be loaded from final location
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'YAPSA' ...
** testing if installed package can be loaded
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
* MD5 sums
packaged installation of 'YAPSA' as YAPSA_1.20.1.zip
* DONE (YAPSA)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'YAPSA' successfully unpacked and MD5 sums checked