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### Running command:
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###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ChromSCape.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings ChromSCape_1.6.0.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/ChromSCape.Rcheck'
* using R version 4.2.1 (2022-06-23 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'ChromSCape/DESCRIPTION' ... OK
* this is package 'ChromSCape' version '1.6.0'
* 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 ... 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  5.5Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    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 ... WARNING
'::' or ':::' import not declared from: 'GenomeInfoDb'
* 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'
enrich_TF_ChEA3_genes: no visible binding for global variable
  'CheA3_TF_nTargets'
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_correlation_PCA_scExp: no visible binding for global variable
  'Component'
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_percent_active_feature_scExp: no visible binding for global
  variable 'group'
plot_percent_active_feature_scExp: no visible binding for global
  variable 'percent_active'
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'
plot_top_TF_scExp: no visible binding for global variable 'TF'
rawfile_ToBigWig: no visible binding for global variable 'filename'
rebin_matrix: no visible global function definition for 'head'
rebin_matrix: no visible binding for global variable 'new_row'
rebin_matrix: no visible binding for global variable 'origin_value'
subset_bam_call_peaks: no visible binding for global variable
  'merged_bam'
Undefined global functions or variables:
  CheA3_TF_nTargets Component Fri_cyto Gain_or_Loss Gene TF V1 V2
  absolute_value annot. cluster clusterConsensus cytoBand filename
  files_dir_list genes group head k merged_bam molecule ncells new_row
  orientation origin_value percent_active run_tsne sample_id
  total_counts
Consider adding
  importFrom("utils", "head")
to your NAMESPACE file.
* 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 ... WARNING
Codoc mismatches from documentation object 'count_coverage':
count_coverage
  Code: function(input, format = "BAM", bins, canonical_chr,
                 n_smoothBin = 5, ref = "hg38", read_size = 101,
                 original_bins = NULL)
  Docs: function(filename, format = "BAM", bins, canonical_chr,
                 n_smoothBin = 5, ref = "hg38", read_size = 101)
  Argument names in code not in docs:
    input original_bins
  Argument names in docs not in code:
    filename
  Mismatches in argument names:
    Position: 1 Code: input Docs: filename

Codoc mismatches from documentation object 'find_clusters_louvain_scExp':
find_clusters_louvain_scExp
  Code: function(scExp, k = 10, resolution = 1, use.dimred = "PCA",
                 type = c("rank", "number", "jaccard")[3], BPPARAM =
                 BiocParallel::bpparam())
  Docs: function(scExp, k = 10, use.dimred = "PCA", type = c("rank",
                 "number", "jaccard")[3], BPPARAM =
                 BiocParallel::bpparam())
  Argument names in code not in docs:
    resolution
  Mismatches in argument names:
    Position: 3 Code: resolution Docs: use.dimred
    Position: 4 Code: use.dimred Docs: type
    Position: 5 Code: type Docs: BPPARAM

Codoc mismatches from documentation object 'generate_coverage_tracks':
generate_coverage_tracks
  Code: function(scExp_cf, input, odir, format = "scBED", ref_genome =
                 c("hg38", "mm10")[1], bin_width = 150, n_smoothBin =
                 5, read_size = 101, progress = NULL)
  Docs: function(scExp_cf, input, odir, input_type = "scBED",
                 ref_genome = c("hg38", "mm10")[1], bin_width = 150,
                 n_smoothBin = 5, read_size = 101, progress = NULL)
  Argument names in code not in docs:
    format
  Argument names in docs not in code:
    input_type
  Mismatches in argument names:
    Position: 4 Code: format Docs: input_type

Codoc mismatches from documentation object 'rawfile_ToBigWig':
rawfile_ToBigWig
  Code: function(input, BigWig_filename, format = "BAM", bin_width =
                 150, n_smoothBin = 5, ref = "hg38", read_size = 101,
                 original_bins = NULL)
  Docs: function(input, BigWig_filename, format = "BAM", bin_width =
                 150, n_smoothBin = 5, ref = "hg38", read_size = 101)
  Argument names in code not in docs:
    original_bins

* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'generate_coverage_tracks'
  'input_type'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 'F:/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)

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' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                       user system elapsed
plot_gain_or_loss_barplots            53.83   0.64   54.50
calculate_CNA                         27.66   1.17   28.83
plot_reduced_dim_scExp_CNA            28.29   0.31   28.61
get_most_variable_cyto                27.69   0.28   27.97
calculate_gain_or_loss                26.88   0.66   27.55
calculate_cyto_mat                    26.20   0.36   26.56
get_cyto_features                     25.59   0.38   25.97
calculate_logRatio_CNA                25.01   0.64   25.67
filter_correlated_cell_scExp          12.03   0.17   30.47
num_cell_after_cor_filt_scExp         11.64   0.23   28.86
CompareedgeRGLM                       11.70   0.10   11.81
create_scDataset_raw                   8.76   0.44    9.21
preprocessing_filtering_and_reduction  8.25   0.02    8.28
import_scExp                           7.44   0.08    7.52
differential_activation                6.64   0.13    6.78
CompareWilcox                          5.44   0.14   52.57
plot_reduced_dim_scExp                 5.49   0.09    5.57
choose_cluster_scExp                   4.45   0.81    5.28
consensus_clustering_scExp             4.32   0.56    5.01
enrich_TF_ChEA3_scExp                  2.20   0.22    8.04
find_clusters_louvain_scExp            1.57   0.13    9.36
* 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: 3 WARNINGs, 5 NOTEs
See
  'F:/biocbuild/bbs-3.15-bioc/meat/ChromSCape.Rcheck/00check.log'
for details.