| Back to Multiple platform build/check report for BioC 3.22: simplified long | 
 | 
This page was generated on 2025-10-30 12:35 -0400 (Thu, 30 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs | 
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4901 | 
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4691 | 
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4637 | 
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 362/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ChromSCape 1.20.0  (landing page) Pacome Prompsy 
 | nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS |  | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | WARNINGS | OK |  | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | WARNINGS | OK |  | ||||||||
| To the developers/maintainers of the ChromSCape package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ChromSCape.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. | 
| Package: ChromSCape | 
| Version: 1.20.0 | 
| 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_1.20.0.tar.gz | 
| StartedAt: 2025-10-30 02:54:52 -0400 (Thu, 30 Oct 2025) | 
| EndedAt: 2025-10-30 03:09:28 -0400 (Thu, 30 Oct 2025) | 
| EllapsedTime: 875.6 seconds | 
| RetCode: 0 | 
| Status: WARNINGS | 
| CheckDir: ChromSCape.Rcheck | 
| Warnings: 1 | 
##############################################################################
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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_1.20.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/ChromSCape.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ChromSCape/DESCRIPTION’ ... OK
* this is package ‘ChromSCape’ version ‘1.20.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 51 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.1.sdk’
* 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 code 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... WARNING
'loadNamespace' or 'requireNamespace' call not declared from: ‘flexdashboard’
* 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 ... 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 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
get_pathway_mat_scExp                 83.436  7.010  90.715
plot_gain_or_loss_barplots            54.513  0.469  55.085
calculate_CNA                         28.753  2.002  30.952
plot_reduced_dim_scExp_CNA            26.634  0.215  26.879
calculate_logRatio_CNA                25.834  0.802  26.677
calculate_gain_or_loss                25.875  0.669  26.592
calculate_cyto_mat                    25.617  0.718  26.372
get_most_variable_cyto                23.627  0.265  23.935
get_cyto_features                     22.222  0.140  22.397
num_cell_after_cor_filt_scExp         12.815  0.129  12.955
filter_correlated_cell_scExp           9.959  0.117  10.100
preprocessing_filtering_and_reduction  9.702  0.162   9.880
import_scExp                           8.311  1.127   9.486
rebin_matrix                           7.895  0.045  24.712
CompareWilcox                          6.972  0.504   6.912
create_scDataset_raw                   6.760  0.577   7.352
differential_activation                5.671  0.068   5.746
CompareedgeRGLM                        5.294  0.367   5.675
enrich_TF_ChEA3_scExp                  1.176  0.096   5.714
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/ChromSCape.Rcheck/00check.log’
for details.
ChromSCape.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ChromSCape ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘ChromSCape’ ... ** this is package ‘ChromSCape’ version ‘1.20.0’ ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.1.sdk’ clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c as_dist.cpp -o as_dist.o clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o ChromSCape.so RcppExports.o as_dist.o -F/Library/Frameworks/R.framework/.. -framework R installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/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)
ChromSCape.Rcheck/tests/testthat.Rout
R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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 2 | SKIP 0 | PASS 11 ]
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 11 ]
> 
> proc.time()
   user  system elapsed 
 40.466   3.795  44.234 
ChromSCape.Rcheck/ChromSCape-Ex.timings
| name | user | system | elapsed | |
| CheA3_TF_nTargets | 0.009 | 0.003 | 0.016 | |
| CompareWilcox | 6.972 | 0.504 | 6.912 | |
| CompareedgeRGLM | 5.294 | 0.367 | 5.675 | |
| annotToCol2 | 1.091 | 0.057 | 1.152 | |
| calculate_CNA | 28.753 | 2.002 | 30.952 | |
| calculate_cyto_mat | 25.617 | 0.718 | 26.372 | |
| calculate_gain_or_loss | 25.875 | 0.669 | 26.592 | |
| calculate_logRatio_CNA | 25.834 | 0.802 | 26.677 | |
| choose_cluster_scExp | 3.594 | 0.841 | 4.460 | |
| colors_scExp | 0.303 | 0.007 | 0.310 | |
| consensus_clustering_scExp | 3.134 | 0.909 | 4.063 | |
| correlation_and_hierarchical_clust_scExp | 0.376 | 0.007 | 0.383 | |
| create_project_folder | 0.001 | 0.002 | 0.003 | |
| create_scDataset_raw | 6.760 | 0.577 | 7.352 | |
| create_scExp | 0.505 | 0.008 | 0.514 | |
| define_feature | 0.164 | 0.005 | 0.169 | |
| detect_samples | 1.022 | 0.080 | 1.105 | |
| differential_activation | 5.671 | 0.068 | 5.746 | |
| differential_analysis_scExp | 3.084 | 0.040 | 3.129 | |
| enrich_TF_ChEA3_genes | 0.550 | 0.185 | 2.129 | |
| enrich_TF_ChEA3_scExp | 1.176 | 0.096 | 5.714 | |
| exclude_features_scExp | 0.471 | 0.010 | 0.482 | |
| feature_annotation_scExp | 1.407 | 0.098 | 1.507 | |
| filter_correlated_cell_scExp | 9.959 | 0.117 | 10.100 | |
| filter_scExp | 0.638 | 0.006 | 0.646 | |
| find_clusters_louvain_scExp | 0.384 | 0.008 | 0.391 | |
| find_top_features | 0.372 | 0.006 | 0.378 | |
| gene_set_enrichment_analysis_scExp | 0.285 | 0.008 | 0.294 | |
| generate_analysis | 0 | 0 | 0 | |
| generate_coverage_tracks | 0.000 | 0.000 | 0.001 | |
| generate_report | 0.001 | 0.000 | 0.001 | |
| getExperimentNames | 0.271 | 0.006 | 0.279 | |
| getMainExperiment | 0.320 | 0.009 | 0.330 | |
| get_cyto_features | 22.222 | 0.140 | 22.397 | |
| get_genomic_coordinates | 0.444 | 0.003 | 0.448 | |
| get_most_variable_cyto | 23.627 | 0.265 | 23.935 | |
| get_pathway_mat_scExp | 83.436 | 7.010 | 90.715 | |
| has_genomic_coordinates | 0.623 | 0.013 | 0.636 | |
| import_scExp | 8.311 | 1.127 | 9.486 | |
| inter_correlation_scExp | 0.377 | 0.020 | 0.398 | |
| intra_correlation_scExp | 0.387 | 0.026 | 0.414 | |
| launchApp | 0.000 | 0.001 | 0.001 | |
| normalize_scExp | 0.455 | 0.026 | 0.481 | |
| num_cell_after_QC_filt_scExp | 0.417 | 0.007 | 0.424 | |
| num_cell_after_cor_filt_scExp | 12.815 | 0.129 | 12.955 | |
| num_cell_before_cor_filt_scExp | 0.271 | 0.019 | 0.291 | |
| num_cell_in_cluster_scExp | 0.460 | 0.008 | 0.468 | |
| num_cell_scExp | 0.340 | 0.003 | 0.344 | |
| plot_cluster_consensus_scExp | 1.156 | 0.020 | 1.179 | |
| plot_correlation_PCA_scExp | 1.304 | 0.073 | 1.381 | |
| plot_coverage_BigWig | 0.271 | 0.010 | 0.282 | |
| plot_differential_summary_scExp | 0.302 | 0.006 | 0.309 | |
| plot_differential_volcano_scExp | 0.383 | 0.014 | 0.398 | |
| plot_distribution_scExp | 0.487 | 0.010 | 0.498 | |
| plot_gain_or_loss_barplots | 54.513 | 0.469 | 55.085 | |
| plot_heatmap_scExp | 0.373 | 0.012 | 0.385 | |
| plot_inter_correlation_scExp | 0.775 | 0.013 | 0.790 | |
| plot_intra_correlation_scExp | 0.739 | 0.009 | 0.750 | |
| plot_most_contributing_features | 0.549 | 0.015 | 0.565 | |
| plot_percent_active_feature_scExp | 0.589 | 0.007 | 0.597 | |
| plot_pie_most_contributing_chr | 0.339 | 0.010 | 0.348 | |
| plot_reduced_dim_scExp | 1.780 | 0.025 | 1.807 | |
| plot_reduced_dim_scExp_CNA | 26.634 | 0.215 | 26.879 | |
| plot_top_TF_scExp | 0.715 | 0.017 | 0.734 | |
| plot_violin_feature_scExp | 0.748 | 0.015 | 0.765 | |
| preprocess_CPM | 0.392 | 0.028 | 0.420 | |
| preprocess_RPKM | 0.423 | 0.025 | 0.448 | |
| preprocess_TFIDF | 0.449 | 0.041 | 0.492 | |
| preprocess_TPM | 0.483 | 0.089 | 0.574 | |
| preprocess_feature_size_only | 0.404 | 0.027 | 0.431 | |
| preprocessing_filtering_and_reduction | 9.702 | 0.162 | 9.880 | |
| read_sparse_matrix | 0 | 0 | 0 | |
| rebin_matrix | 7.895 | 0.045 | 24.712 | |
| reduce_dims_scExp | 1.840 | 0.062 | 1.905 | |
| scExp | 1.199 | 0.042 | 1.244 | |
| subsample_scExp | 0.612 | 0.036 | 0.649 | |
| subset_bam_call_peaks | 0.001 | 0.001 | 0.000 | |
| summary_DA | 0.307 | 0.006 | 0.313 | |
| swapAltExp_sameColData | 0.370 | 0.010 | 0.381 | |
| table_enriched_genes_scExp | 0.236 | 0.009 | 0.245 | |
| wrapper_Signac_FeatureMatrix | 0.001 | 0.000 | 0.000 | |