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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ChromSCape.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ChromSCape_1.6.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/ChromSCape.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-apple-darwin17.0 (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 for sufficient/correct file permissions ... OK
* checking whether package ‘ChromSCape’ 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 ... 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 is not available
* 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            99.426  0.459 105.833
calculate_CNA                         47.532  1.693  50.019
plot_reduced_dim_scExp_CNA            48.215  0.195  51.213
calculate_cyto_mat                    46.453  0.567  48.983
get_most_variable_cyto                46.056  0.395  48.396
calculate_gain_or_loss                45.143  0.499  45.897
calculate_logRatio_CNA                43.280  0.495  43.855
get_cyto_features                     41.166  0.398  41.683
num_cell_after_cor_filt_scExp         11.393  0.555  12.465
filter_correlated_cell_scExp          10.799  0.576  11.367
preprocessing_filtering_and_reduction 11.132  0.118  11.796
differential_activation               11.055  0.060  11.135
create_scDataset_raw                   9.961  0.494  10.470
CompareedgeRGLM                        9.411  0.380   9.804
CompareWilcox                          7.524  1.053   6.487
plot_reduced_dim_scExp                 8.337  0.063   9.146
import_scExp                           6.987  0.115   7.415
choose_cluster_scExp                   6.031  0.658   6.715
differential_analysis_scExp            5.788  0.023   5.818
consensus_clustering_scExp             5.181  0.612   5.812
plot_violin_feature_scExp              5.237  0.038   5.557
enrich_TF_ChEA3_scExp                  1.999  0.089   7.919
* 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, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/ChromSCape.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ChromSCape
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘ChromSCape’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c as_dist.cpp -o as_dist.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o ChromSCape.so RcppExports.o as_dist.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.2/Resources/library/00LOCK-ChromSCape/00new/ChromSCape/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ChromSCape)

R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 1 | SKIP 0 | PASS 11 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 11 ]
> 
> proc.time()
   user  system elapsed 
 58.338   3.779  64.252