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### Running command:
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### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ChromSCape.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings ChromSCape_1.9.0.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/ChromSCape.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 10.4.0
GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'ChromSCape/DESCRIPTION' ... OK
* this is package 'ChromSCape' version '1.9.0'
* 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
* used C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
* 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
'library' or 'require' call not declared from: 'dplyr'
'library' or 'require' call to 'dplyr' in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
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 global function definition for 'head'
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'
rebin_helper: no visible binding for global variable 'new_row'
rebin_helper: no visible binding for global variable 'origin_value'
rebin_matrix: no visible binding for global variable 'group'
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 cluster clusterConsensus cytoBand 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 'generate_analysis':
generate_analysis
Code: function(input_data_folder, analysis_name = "Analysis_1",
output_directory = "./", input_data_type = c("scBED",
"DenseMatrix", "SparseMatrix", "scBAM")[1],
feature_count_on = c("bins", "genebody", "peaks")[1],
feature_count_parameter = 50000, rebin_sparse_matrix =
FALSE, ref_genome = c("hg38", "mm10")[1], run =
c("filter", "CNA", "cluster", "consensus", "coverage",
"DA", "GSA", "report")[c(1, 3, 5, 6, 7, 8)],
min_reads_per_cell = 1000, max_quantile_read_per_cell
= 99, n_top_features = 40000, norm_type = "CPM",
subsample_n = NULL, exclude_regions = NULL, n_clust =
NULL, corr_threshold = 99, percent_correlation = 1,
maxK = 10, qval.th = 0.1, logFC.th = 1,
enrichment_qval = 0.1, doBatchCorr = FALSE, batch_sels
= NULL, control_samples_CNA = NULL, genes_to_plot =
c("Krt8", "Krt5", "Tgfb1", "Foxq1", "Cdkn2b",
"Cdkn2a", "chr7:15000000-20000000"))
Docs: function(input_data_folder, analysis_name = "Analysis_1",
output_directory = "./", input_data_type = c("scBED",
"DenseMatrix", "SparseMatrix", "scBAM")[1],
rebin_sparse_matrix = FALSE, feature_count_on =
c("bins", "genebody", "peaks")[1],
feature_count_parameter = 50000, ref_genome =
c("hg38", "mm10")[1], run = c("filter", "CNA",
"cluster", "consensus", "peak_call", "coverage", "DA",
"GSA", "report")[c(1, 3, 6, 7, 8, 9)],
min_reads_per_cell = 1000, max_quantile_read_per_cell
= 99, n_top_features = 40000, norm_type = "CPM",
subsample_n = NULL, exclude_regions = NULL, n_clust =
NULL, corr_threshold = 99, percent_correlation = 1,
maxK = 10, qval.th = 0.1, logFC.th = 1,
enrichment_qval = 0.1, doBatchCorr = FALSE, batch_sels
= NULL, control_samples_CNA = NULL, genes_to_plot =
c("Krt8", "Krt5", "Tgfb1", "Foxq1", "Cdkn2b",
"Cdkn2a", "chr7:15000000-20000000"))
Mismatches in argument names:
Position: 5 Code: feature_count_on Docs: rebin_sparse_matrix
Position: 6 Code: feature_count_parameter Docs: feature_count_on
Position: 7 Code: rebin_sparse_matrix Docs: feature_count_parameter
Mismatches in argument default values:
Name: 'run'
Code: c("filter", "CNA", "cluster", "consensus", "coverage", "DA",
"GSA", "report")[c(1, 3, 5, 6, 7, 8)]
Docs: c("filter", "CNA", "cluster", "consensus", "peak_call", "coverage",
"DA", "GSA", "report")[c(1, 3, 6, 7, 8, 9)]
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'rebin_matrix'
'rebin_function'
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-3.17-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 nor [v]sprintf. 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 44.77 0.65 45.50
get_pathway_mat_scExp 37.64 3.00 40.75
calculate_CNA 21.65 1.37 23.09
plot_reduced_dim_scExp_CNA 22.11 0.22 22.41
calculate_gain_or_loss 21.12 0.51 21.65
calculate_cyto_mat 20.03 0.60 20.66
get_most_variable_cyto 20.08 0.25 20.42
calculate_logRatio_CNA 19.47 0.53 20.03
get_cyto_features 17.96 0.23 18.22
CompareedgeRGLM 11.29 0.21 11.48
num_cell_after_cor_filt_scExp 9.07 0.12 22.97
filter_correlated_cell_scExp 8.37 0.17 21.40
preprocessing_filtering_and_reduction 7.44 0.04 7.53
create_scDataset_raw 6.18 0.30 6.50
import_scExp 5.63 0.08 5.70
rebin_matrix 4.89 0.02 19.65
CompareWilcox 3.49 0.26 38.41
enrich_TF_ChEA3_scExp 1.61 0.22 7.67
* 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-3.17-bioc-rtools43/meat/ChromSCape.Rcheck/00check.log'
for details.