Pacome Prompsy
| Snapshot Date: 2026-04-12 13:40 -0400 (Sun, 12 Apr 2026) |
| git_url: https://git.bioconductor.org/packages/ChromSCape |
| git_branch: devel |
| git_last_commit: 374f36e |
| git_last_commit_date: 2026-04-08 12:23:03 -0400 (Wed, 08 Apr 2026) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-04-13 11:35 -0400 (Mon, 13 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 alpha (2026-04-05 r89794) | 4919 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 alpha (2026-04-08 r89818) | 4632 |
| 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 364/2390 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ChromSCape 1.21.1 (landing page) Pacome Prompsy
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| See other builds for ChromSCape in R Universe. | ||||||||||||||
|
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: 1.21.1 |
| 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_1.21.1.tar.gz |
| StartedAt: 2026-04-12 18:54:50 -0400 (Sun, 12 Apr 2026) |
| EndedAt: 2026-04-12 19:00:05 -0400 (Sun, 12 Apr 2026) |
| EllapsedTime: 314.8 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_1.21.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/ChromSCape.Rcheck’
* using R version 4.6.0 alpha (2026-04-08 r89818)
* using platform: aarch64-apple-darwin23
* R was compiled by
Apple clang version 17.0.0 (clang-1700.3.19.1)
GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-04-12 22:54:50 UTC
* using option ‘--no-vignettes’
* checking for file ‘ChromSCape/DESCRIPTION’ ... OK
* this is package ‘ChromSCape’ version ‘1.21.1’
* 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 17.0.0 (clang-1700.6.4.2)’
* used SDK: ‘MacOSX26.2.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 ... INFO
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 32.019 0.680 33.307
plot_gain_or_loss_barplots 17.268 0.162 17.749
calculate_CNA 7.551 0.581 8.205
calculate_logRatio_CNA 7.527 0.233 7.979
plot_reduced_dim_scExp_CNA 7.627 0.040 7.683
calculate_gain_or_loss 7.095 0.197 7.367
calculate_cyto_mat 6.940 0.198 7.200
get_most_variable_cyto 6.942 0.033 7.045
get_cyto_features 5.754 0.025 5.839
num_cell_after_cor_filt_scExp 5.639 0.045 5.784
rebin_matrix 3.470 0.023 10.354
* 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, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.23-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/4.6/Resources/library’ * installing *source* package ‘ChromSCape’ ... ** this is package ‘ChromSCape’ version ‘1.21.1’ ** using staged installation ** libs using C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’ using SDK: ‘MacOSX26.2.sdk’ clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c as_dist.cpp -o as_dist.o clang++ -arch arm64 -std=gnu++20 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o ChromSCape.so RcppExports.o as_dist.o -F/Library/Frameworks/R.framework/.. -framework R installing to /Library/Frameworks/R.framework/Versions/4.6/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 4.6.0 alpha (2026-04-08 r89818)
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23
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
15.820 0.859 16.816
ChromSCape.Rcheck/ChromSCape-Ex.timings
| name | user | system | elapsed | |
| CheA3_TF_nTargets | 0.003 | 0.001 | 0.003 | |
| CompareWilcox | 2.829 | 0.292 | 2.970 | |
| CompareedgeRGLM | 1.493 | 0.049 | 1.547 | |
| annotToCol2 | 0.332 | 0.026 | 0.359 | |
| calculate_CNA | 7.551 | 0.581 | 8.205 | |
| calculate_cyto_mat | 6.940 | 0.198 | 7.200 | |
| calculate_gain_or_loss | 7.095 | 0.197 | 7.367 | |
| calculate_logRatio_CNA | 7.527 | 0.233 | 7.979 | |
| choose_cluster_scExp | 1.330 | 0.065 | 1.412 | |
| colors_scExp | 0.133 | 0.003 | 0.139 | |
| consensus_clustering_scExp | 1.241 | 0.057 | 1.324 | |
| correlation_and_hierarchical_clust_scExp | 0.132 | 0.002 | 0.134 | |
| create_project_folder | 0.000 | 0.002 | 0.002 | |
| create_scDataset_raw | 2.989 | 0.077 | 3.110 | |
| create_scExp | 0.164 | 0.003 | 0.171 | |
| define_feature | 0.057 | 0.002 | 0.059 | |
| detect_samples | 0.503 | 0.004 | 0.519 | |
| differential_activation | 2.006 | 0.016 | 2.053 | |
| differential_analysis_scExp | 1.068 | 0.007 | 1.088 | |
| enrich_TF_ChEA3_genes | 0.214 | 0.054 | 1.550 | |
| enrich_TF_ChEA3_scExp | 0.435 | 0.032 | 4.818 | |
| exclude_features_scExp | 0.148 | 0.009 | 0.156 | |
| feature_annotation_scExp | 0.510 | 0.023 | 0.538 | |
| filter_correlated_cell_scExp | 4.482 | 0.016 | 4.532 | |
| filter_scExp | 0.171 | 0.004 | 0.176 | |
| find_clusters_louvain_scExp | 0.131 | 0.002 | 0.134 | |
| find_top_features | 0.137 | 0.001 | 0.139 | |
| gene_set_enrichment_analysis_scExp | 0.099 | 0.001 | 0.100 | |
| generate_analysis | 0 | 0 | 0 | |
| generate_coverage_tracks | 0 | 0 | 0 | |
| generate_report | 0 | 0 | 0 | |
| getExperimentNames | 0.109 | 0.002 | 0.111 | |
| getMainExperiment | 0.124 | 0.002 | 0.128 | |
| get_cyto_features | 5.754 | 0.025 | 5.839 | |
| get_genomic_coordinates | 0.124 | 0.003 | 0.127 | |
| get_most_variable_cyto | 6.942 | 0.033 | 7.045 | |
| get_pathway_mat_scExp | 32.019 | 0.680 | 33.307 | |
| has_genomic_coordinates | 0.208 | 0.004 | 0.212 | |
| import_scExp | 3.348 | 0.018 | 3.397 | |
| inter_correlation_scExp | 0.147 | 0.004 | 0.151 | |
| intra_correlation_scExp | 0.146 | 0.003 | 0.148 | |
| launchApp | 0.000 | 0.001 | 0.000 | |
| normalize_scExp | 0.133 | 0.007 | 0.140 | |
| num_cell_after_QC_filt_scExp | 0.137 | 0.002 | 0.139 | |
| num_cell_after_cor_filt_scExp | 5.639 | 0.045 | 5.784 | |
| num_cell_before_cor_filt_scExp | 0.116 | 0.004 | 0.124 | |
| num_cell_in_cluster_scExp | 0.188 | 0.008 | 0.205 | |
| num_cell_scExp | 0.136 | 0.005 | 0.144 | |
| plot_cluster_consensus_scExp | 0.384 | 0.006 | 0.399 | |
| plot_correlation_PCA_scExp | 0.441 | 0.007 | 0.457 | |
| plot_coverage_BigWig | 0.098 | 0.002 | 0.100 | |
| plot_differential_summary_scExp | 0.107 | 0.001 | 0.109 | |
| plot_differential_volcano_scExp | 0.179 | 0.011 | 0.199 | |
| plot_distribution_scExp | 0.197 | 0.004 | 0.206 | |
| plot_gain_or_loss_barplots | 17.268 | 0.162 | 17.749 | |
| plot_heatmap_scExp | 0.137 | 0.003 | 0.141 | |
| plot_inter_correlation_scExp | 0.243 | 0.004 | 0.250 | |
| plot_intra_correlation_scExp | 0.247 | 0.002 | 0.252 | |
| plot_most_contributing_features | 0.187 | 0.002 | 0.191 | |
| plot_percent_active_feature_scExp | 0.200 | 0.003 | 0.208 | |
| plot_pie_most_contributing_chr | 0.129 | 0.004 | 0.136 | |
| plot_reduced_dim_scExp | 0.571 | 0.006 | 0.580 | |
| plot_reduced_dim_scExp_CNA | 7.627 | 0.040 | 7.683 | |
| plot_top_TF_scExp | 0.228 | 0.002 | 0.230 | |
| plot_violin_feature_scExp | 0.256 | 0.003 | 0.258 | |
| preprocess_CPM | 0.133 | 0.013 | 0.145 | |
| preprocess_RPKM | 0.136 | 0.010 | 0.147 | |
| preprocess_TFIDF | 0.133 | 0.012 | 0.146 | |
| preprocess_TPM | 0.161 | 0.011 | 0.175 | |
| preprocess_feature_size_only | 0.131 | 0.010 | 0.145 | |
| preprocessing_filtering_and_reduction | 4.142 | 0.020 | 4.192 | |
| read_sparse_matrix | 0 | 0 | 0 | |
| rebin_matrix | 3.470 | 0.023 | 10.354 | |
| reduce_dims_scExp | 0.614 | 0.009 | 0.625 | |
| scExp | 0.423 | 0.013 | 0.448 | |
| subsample_scExp | 0.191 | 0.008 | 0.199 | |
| subset_bam_call_peaks | 0 | 0 | 0 | |
| summary_DA | 0.114 | 0.002 | 0.118 | |
| swapAltExp_sameColData | 0.126 | 0.002 | 0.128 | |
| table_enriched_genes_scExp | 0.119 | 0.004 | 0.129 | |
| wrapper_Signac_FeatureMatrix | 0 | 0 | 0 | |