##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ChromSCape.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings ChromSCape_1.5.22.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/ChromSCape.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 'ChromSCape/DESCRIPTION' ... OK
* this is package 'ChromSCape' version '1.5.22'
* 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:
  .BBSoptions
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 'ChromSCape' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    www    2.1Mb
* 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 ... NOTE
CompareWilcox: no visible binding for global variable 'annot.'
bams_to_matrix_indexes: no visible binding for global variable
  'files_dir_list'
filter_correlated_cell_scExp: no visible binding for global variable
  'run_tsne'
generate_analysis: no visible binding for global variable 'k'
generate_analysis: no visible binding for global variable
  'clusterConsensus'
get_most_variable_cyto: no visible binding for global variable
  'cytoBand'
get_most_variable_cyto: no visible binding for global variable
  'Fri_cyto'
num_cell_after_QC_filt_scExp: no visible binding for global variable
  'sample_id'
num_cell_after_QC_filt_scExp: no visible binding for global variable
  'total_counts'
num_cell_scExp: no visible binding for global variable 'sample_id'
num_cell_scExp: no visible binding for global variable 'total_counts'
plot_coverage_BigWig: no visible binding for global variable 'score'
plot_coverage_BigWig: no visible binding for global variable 'molecule'
plot_coverage_BigWig: no visible binding for global variable
  'orientation'
plot_coverage_BigWig: no visible binding for global variable 'Gene'
plot_gain_or_loss_barplots: no visible binding for global variable
  'Gain_or_Loss'
plot_gain_or_loss_barplots: no visible binding for global variable
  'ncells'
plot_gain_or_loss_barplots: no visible binding for global variable
  'cytoBand'
plot_most_contributing_features: no visible binding for global variable
  'genes'
plot_pie_most_contributing_chr: no visible binding for global variable
  'absolute_value'
plot_reduced_dim_scExp: no visible binding for global variable 'V1'
plot_reduced_dim_scExp: no visible binding for global variable 'V2'
plot_reduced_dim_scExp: no visible binding for global variable
  'cluster'
subset_bam_call_peaks: no visible binding for global variable
  'merged_bam'
Undefined global functions or variables:
  Fri_cyto Gain_or_Loss Gene V1 V2 absolute_value annot. cluster
  clusterConsensus cytoBand files_dir_list genes k merged_bam molecule
  ncells orientation run_tsne sample_id score total_counts
* checking Rd files ... NOTE
prepare_Rd: raw_counts_to_sparse_matrix.Rd:6-8: Dropping empty section \source
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'D:/biocbuild/bbs-3.15-bioc/R/library/ChromSCape/libs/x64/ChromSCape.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... NOTE
Files named as vignettes but with no recognized vignette engine:
   'vignettes/PairedTag_Zhu_H3K4me1.Rmd'
   'vignettes/scChIC_Ku_H3K4me3.Rmd'
(Is a VignetteBuilder field missing?)
* checking examples ... ERROR
Running examples in 'ChromSCape-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: differential_analysis_scExp
> ### Title: Runs differential analysis between cell clusters
> ### Aliases: differential_analysis_scExp
> 
> ### ** Examples
> 
> data("scExp")
> scExp_cf = differential_analysis_scExp(scExp)
Warning in .Internal(gc(verbose, reset, full)) :
  closing unused connection 15 (<-riesling1:11417)
Warning in .Internal(gc(verbose, reset, full)) :
  closing unused connection 14 (<-riesling1:11417)
Warning in .Internal(gc(verbose, reset, full)) :
  closing unused connection 13 (<-riesling1:11417)
Warning in .Internal(gc(verbose, reset, full)) :
  closing unused connection 12 (<-riesling1:11417)
Warning in .Internal(gc(verbose, reset, full)) :
  closing unused connection 11 (<-riesling1:11417)
Warning in .Internal(gc(verbose, reset, full)) :
  closing unused connection 10 (<-riesling1:11417)
Warning in .Internal(gc(verbose, reset, full)) :
  closing unused connection 9 (<-riesling1:11417)
Warning in .Internal(gc(verbose, reset, full)) :
  closing unused connection 8 (<-riesling1:11417)
Warning in .Internal(gc(verbose, reset, full)) :
  closing unused connection 7 (<-riesling1:11417)
Warning in .Internal(gc(verbose, reset, full)) :
  closing unused connection 6 (<-riesling1:11417)
Warning in .Internal(gc(verbose, reset, full)) :
  closing unused connection 5 (<-riesling1:11417)
Warning in .Internal(gc(verbose, reset, full)) :
  closing unused connection 4 (<-riesling1:11417)
Error in `[.data.frame`(res, , logFC.col) : undefined columns selected
Calls: differential_analysis_scExp -> [ -> [.data.frame
Execution halted
* 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 ERROR, 6 NOTEs
See
  'D:/biocbuild/bbs-3.15-bioc/meat/ChromSCape.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL ChromSCape
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'ChromSCape' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c as_dist.cpp -o as_dist.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o ChromSCape.dll tmp.def RcppExports.o as_dist.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-ChromSCape/00new/ChromSCape/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ChromSCape'
    finding HTML links ... done
    CompareWilcox                           html  
    CompareedgeRGLM                         html  
    DA_custom                               html  
    DA_one_vs_rest_fun                      html  
    DA_pairwise                             html  
    H1proportion                            html  
    annotToCol2                             html  
    annotation_from_merged_peaks            html  
    anocol_binary                           html  
    anocol_categorical                      html  
    bams_to_matrix_indexes                  html  
    beds_to_matrix_indexes                  html  
    calculate_CNA                           html  
    calculate_cyto_mat                      html  
    calculate_gain_or_loss                  html  
    calculate_logRatio_CNA                  html  
    call_macs2_merge_peaks                  html  
    changeRange                             html  
    check_correct_datamatrix                html  
    choose_cluster_scExp                    html  
    choose_perplexity                       html  
    col2hex                                 html  
    colors_scExp                            html  
    combine_datamatrix                      html  
    combine_enrichmentTests                 html  
    concatenate_scBed_into_clusters         html  
    consensus_clustering_scExp              html  
    correlation_and_hierarchical_clust_scExp
                                            html  
    count_coverage                          html  
    create_project_folder                   html  
    create_sample_name_mat                  html  
    create_scDataset_raw                    html  
    create_scExp                            html  
    define_feature                          html  
    detect_samples                          html  
    differential_activation_scExp           html  
    differential_analysis_scExp             html  
    distPearson                             html  
    enrichmentTest                          html  
    exclude_features_scExp                  html  
    feature_annotation_scExp                html  
    filter_correlated_cell_scExp            html  
    filter_genes_with_refined_peak_annotation
                                            html  
    filter_scExp                            html  
    find_top_features                       html  
    gene_set_enrichment_analysis_scExp      html  
    generate_analysis                       html  
    generate_count_matrix                   html  
    generate_coverage_tracks                html  
    generate_feature_names                  html  
    generate_report                         html  
    getExperimentNames                      html  
    getMainExperiment                       html  
    get_color_dataframe_from_input          html  
    get_cyto_features                       html  
    get_genomic_coordinates                 html  
    get_most_variable_cyto                  html  
    gg_fill_hue                             html  
    groupMat                                html  
    has_genomic_coordinates                 html  
    hclustAnnotHeatmapPlot                  html  
    hg38.GeneTSS                            html  
    hg38.chromosomes                        html  
    hg38.cytoBand                           html  
    imageCol                                html  
    import_count_input_files                html  
    import_scExp                            html  
    index_peaks_barcodes_to_matrix_indexes
                                            html  
    inter_correlation_scExp                 html  
    intra_correlation_scExp                 html  
    launchApp                               html  
    load_MSIGdb                             html  
    merge_MACS2_peaks                       html  
    mm10.GeneTSS                            html  
    mm10.chromosomes                        html  
    mm10.cytoBand                           html  
    normalize_scExp                         html  
    num_cell_after_QC_filt_scExp            html  
    num_cell_after_cor_filt_scExp           html  
    num_cell_before_cor_filt_scExp          html  
    num_cell_in_cluster_scExp               html  
    num_cell_scExp                          html  
    pca_irlba_for_sparseMatrix              html  
    peaks_to_bins                           html  
    plot_cluster_consensus_scExp            html  
    plot_coverage_BigWig                    html  
    plot_differential_H1_scExp              html  
    plot_differential_summary_scExp         html  
    plot_differential_volcano_scExp         html  
    plot_distribution_scExp                 html  
    plot_gain_or_loss_barplots              html  
    plot_heatmap_scExp                      html  
    plot_inter_correlation_scExp            html  
    plot_intra_correlation_scExp            html  
    plot_most_contributing_features         html  
    plot_pie_most_contributing_chr          html  
    plot_reduced_dim_scExp                  html  
    plot_reduced_dim_scExp_CNA              html  
    preprocess_CPM                          html  
    preprocess_RPKM                         html  
    preprocess_TFIDF                        html  
    preprocess_TPM                          html  
    preprocess_feature_size_only            html  
    preprocessing_filtering_and_reduction   html  
    raw_counts_to_sparse_matrix             html  
    rawfile_ToBigWig                        html  
    read_count_mat_with_separated_chr_start_end
                                            html  
    read_sparse_matrix                      html  
    reduce_dim_batch_correction             html  
    reduce_dims_scExp                       html  
    remove_chr_M_fun                        html  
    remove_non_canonical_fun                html  
    results_enrichmentTest                  html  
    retrieve_top_bot_features_pca           html  
    run_pairwise_tests                      html  
    run_tsne_scExp                          html  
    scExp                                   html  
    separate_BAM_into_clusters              html  
    separator_count_mat                     html  
    smoothBin                               html  
    subsample_scExp                         html  
    subset_bam_call_peaks                   html  
    swapAltExp_sameColData                  html  
    table_enriched_genes_scExp              html  
    warning_DA                              html  
    warning_filter_correlated_cell_scExp    html  
    warning_plot_reduced_dim_scExp          html  
    warning_raw_counts_to_sparse_matrix     html  
    wrapper_Signac_FeatureMatrix            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 (ChromSCape)
Making 'packages.html' ... 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(ChromSCape)
> 
> test_check("ChromSCape")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 11 ]
> 
> proc.time()
   user  system elapsed 
  29.18    4.23   56.68