Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-09-26 12:04 -0400 (Fri, 26 Sep 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" | 4831 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4619 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4563 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4563 |
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 356/2334 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ChromSCape 1.19.1 (landing page) Pacome Prompsy
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | WARNINGS | ||||||||||
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: 1.19.1 |
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_1.19.1.tar.gz |
StartedAt: 2025-09-25 20:06:10 -0400 (Thu, 25 Sep 2025) |
EndedAt: 2025-09-25 20:22:03 -0400 (Thu, 25 Sep 2025) |
EllapsedTime: 953.2 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: ChromSCape.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### 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_1.19.1.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 ‘1.19.1’ * 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 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 92.786 8.868 102.459 plot_gain_or_loss_barplots 59.904 0.558 60.771 calculate_CNA 29.809 1.813 31.777 plot_reduced_dim_scExp_CNA 29.761 0.266 30.191 calculate_logRatio_CNA 28.630 0.896 29.723 calculate_cyto_mat 28.385 1.050 29.671 calculate_gain_or_loss 28.193 0.700 29.070 get_most_variable_cyto 27.081 0.246 27.507 get_cyto_features 24.632 0.194 25.014 num_cell_after_cor_filt_scExp 13.810 0.163 14.039 preprocessing_filtering_and_reduction 10.651 0.242 10.923 filter_correlated_cell_scExp 10.548 0.105 10.702 import_scExp 8.492 1.175 9.744 rebin_matrix 8.239 0.084 26.331 create_scDataset_raw 7.448 0.546 8.055 CompareWilcox 7.080 0.540 7.096 differential_activation 6.451 0.070 6.574 CompareedgeRGLM 5.389 0.349 5.763 enrich_TF_ChEA3_scExp 1.289 0.098 5.196 enrich_TF_ChEA3_genes 0.606 0.195 8.207 * 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 ‘1.19.1’ ** 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 41.768 3.395 45.295
ChromSCape.Rcheck/ChromSCape-Ex.timings
name | user | system | elapsed | |
CheA3_TF_nTargets | 0.006 | 0.002 | 0.008 | |
CompareWilcox | 7.080 | 0.540 | 7.096 | |
CompareedgeRGLM | 5.389 | 0.349 | 5.763 | |
annotToCol2 | 1.107 | 0.049 | 1.162 | |
calculate_CNA | 29.809 | 1.813 | 31.777 | |
calculate_cyto_mat | 28.385 | 1.050 | 29.671 | |
calculate_gain_or_loss | 28.193 | 0.700 | 29.070 | |
calculate_logRatio_CNA | 28.630 | 0.896 | 29.723 | |
choose_cluster_scExp | 3.837 | 0.511 | 4.387 | |
colors_scExp | 0.378 | 0.009 | 0.389 | |
consensus_clustering_scExp | 3.433 | 0.562 | 4.045 | |
correlation_and_hierarchical_clust_scExp | 0.419 | 0.007 | 0.429 | |
create_project_folder | 0.001 | 0.002 | 0.003 | |
create_scDataset_raw | 7.448 | 0.546 | 8.055 | |
create_scExp | 0.534 | 0.008 | 0.543 | |
define_feature | 0.159 | 0.007 | 0.167 | |
detect_samples | 1.170 | 0.059 | 1.236 | |
differential_activation | 6.451 | 0.070 | 6.574 | |
differential_analysis_scExp | 3.410 | 0.034 | 3.468 | |
enrich_TF_ChEA3_genes | 0.606 | 0.195 | 8.207 | |
enrich_TF_ChEA3_scExp | 1.289 | 0.098 | 5.196 | |
exclude_features_scExp | 0.540 | 0.007 | 0.551 | |
feature_annotation_scExp | 1.568 | 0.061 | 1.638 | |
filter_correlated_cell_scExp | 10.548 | 0.105 | 10.702 | |
filter_scExp | 0.659 | 0.009 | 0.671 | |
find_clusters_louvain_scExp | 0.412 | 0.010 | 0.423 | |
find_top_features | 0.414 | 0.008 | 0.424 | |
gene_set_enrichment_analysis_scExp | 0.288 | 0.006 | 0.297 | |
generate_analysis | 0 | 0 | 0 | |
generate_coverage_tracks | 0.000 | 0.001 | 0.000 | |
generate_report | 0 | 0 | 0 | |
getExperimentNames | 0.331 | 0.006 | 0.338 | |
getMainExperiment | 0.401 | 0.009 | 0.413 | |
get_cyto_features | 24.632 | 0.194 | 25.014 | |
get_genomic_coordinates | 0.479 | 0.007 | 0.491 | |
get_most_variable_cyto | 27.081 | 0.246 | 27.507 | |
get_pathway_mat_scExp | 92.786 | 8.868 | 102.459 | |
has_genomic_coordinates | 0.702 | 0.014 | 0.719 | |
import_scExp | 8.492 | 1.175 | 9.744 | |
inter_correlation_scExp | 0.441 | 0.029 | 0.474 | |
intra_correlation_scExp | 0.448 | 0.017 | 0.466 | |
launchApp | 0 | 0 | 0 | |
normalize_scExp | 0.480 | 0.025 | 0.508 | |
num_cell_after_QC_filt_scExp | 0.507 | 0.006 | 0.516 | |
num_cell_after_cor_filt_scExp | 13.810 | 0.163 | 14.039 | |
num_cell_before_cor_filt_scExp | 0.298 | 0.014 | 0.314 | |
num_cell_in_cluster_scExp | 0.502 | 0.008 | 0.514 | |
num_cell_scExp | 0.418 | 0.005 | 0.424 | |
plot_cluster_consensus_scExp | 1.309 | 0.017 | 1.334 | |
plot_correlation_PCA_scExp | 1.525 | 0.048 | 1.579 | |
plot_coverage_BigWig | 0.280 | 0.012 | 0.294 | |
plot_differential_summary_scExp | 0.311 | 0.006 | 0.319 | |
plot_differential_volcano_scExp | 0.364 | 0.021 | 0.387 | |
plot_distribution_scExp | 0.524 | 0.011 | 0.536 | |
plot_gain_or_loss_barplots | 59.904 | 0.558 | 60.771 | |
plot_heatmap_scExp | 0.412 | 0.015 | 0.431 | |
plot_inter_correlation_scExp | 0.860 | 0.018 | 0.884 | |
plot_intra_correlation_scExp | 0.825 | 0.019 | 0.847 | |
plot_most_contributing_features | 0.616 | 0.014 | 0.633 | |
plot_percent_active_feature_scExp | 0.692 | 0.016 | 0.712 | |
plot_pie_most_contributing_chr | 0.362 | 0.009 | 0.373 | |
plot_reduced_dim_scExp | 2.033 | 0.038 | 2.086 | |
plot_reduced_dim_scExp_CNA | 29.761 | 0.266 | 30.191 | |
plot_top_TF_scExp | 0.764 | 0.015 | 0.783 | |
plot_violin_feature_scExp | 0.811 | 0.037 | 0.865 | |
preprocess_CPM | 0.480 | 0.033 | 0.515 | |
preprocess_RPKM | 0.516 | 0.042 | 0.562 | |
preprocess_TFIDF | 0.473 | 0.026 | 0.505 | |
preprocess_TPM | 0.544 | 0.077 | 0.625 | |
preprocess_feature_size_only | 0.439 | 0.027 | 0.468 | |
preprocessing_filtering_and_reduction | 10.651 | 0.242 | 10.923 | |
read_sparse_matrix | 0 | 0 | 0 | |
rebin_matrix | 8.239 | 0.084 | 26.331 | |
reduce_dims_scExp | 1.966 | 0.060 | 2.033 | |
scExp | 1.196 | 0.027 | 1.231 | |
subsample_scExp | 0.656 | 0.041 | 0.700 | |
subset_bam_call_peaks | 0 | 0 | 0 | |
summary_DA | 0.319 | 0.013 | 0.334 | |
swapAltExp_sameColData | 0.368 | 0.012 | 0.382 | |
table_enriched_genes_scExp | 0.285 | 0.019 | 0.307 | |
wrapper_Signac_FeatureMatrix | 0.000 | 0.001 | 0.001 | |