Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-30 12:04 -0400 (Sat, 30 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4824 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4615 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4562 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4541 |
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 353/2320 | 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: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:ChromSCape.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings ChromSCape_1.19.1.tar.gz |
StartedAt: 2025-08-29 21:13:31 -0400 (Fri, 29 Aug 2025) |
EndedAt: 2025-08-29 21:26:13 -0400 (Fri, 29 Aug 2025) |
EllapsedTime: 761.9 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: ChromSCape.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:ChromSCape.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings ChromSCape_1.19.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/ChromSCape.Rcheck’ * using R version 4.5.1 (2025-06-13) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.3 LTS * using session charset: UTF-8 * 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: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ * checking installed package size ... INFO installed size is 5.8Mb sub-directories of 1Mb or more: data 1.7Mb 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 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 loading without being on the library search path ... 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 70.763 3.206 73.973 plot_gain_or_loss_barplots 44.871 0.343 45.217 calculate_CNA 22.264 0.943 23.207 plot_reduced_dim_scExp_CNA 22.388 0.112 22.501 get_most_variable_cyto 22.000 0.236 22.237 calculate_gain_or_loss 21.278 0.439 21.718 calculate_cyto_mat 21.136 0.471 21.609 calculate_logRatio_CNA 20.616 0.377 20.994 get_cyto_features 17.980 0.147 18.128 num_cell_after_cor_filt_scExp 12.174 0.069 12.226 filter_correlated_cell_scExp 9.194 0.118 9.298 preprocessing_filtering_and_reduction 8.896 0.073 8.963 import_scExp 7.040 0.050 7.092 rebin_matrix 6.673 0.090 20.650 CompareedgeRGLM 5.824 0.340 5.887 create_scDataset_raw 5.362 0.222 5.584 CompareWilcox 5.100 0.288 5.163 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 3 NOTEs See ‘/home/biocbuild/bbs-3.22-bioc/meat/ChromSCape.Rcheck/00check.log’ for details.
ChromSCape.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL ChromSCape ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘ChromSCape’ ... ** this is package ‘ChromSCape’ version ‘1.19.1’ ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c as_dist.cpp -o as_dist.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o ChromSCape.so RcppExports.o as_dist.o -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.22-bioc/R/site-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 (2025-06-13) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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 36.769 2.434 38.985
ChromSCape.Rcheck/ChromSCape-Ex.timings
name | user | system | elapsed | |
CheA3_TF_nTargets | 0.034 | 0.000 | 0.033 | |
CompareWilcox | 5.100 | 0.288 | 5.163 | |
CompareedgeRGLM | 5.824 | 0.340 | 5.887 | |
annotToCol2 | 0.845 | 0.005 | 0.850 | |
calculate_CNA | 22.264 | 0.943 | 23.207 | |
calculate_cyto_mat | 21.136 | 0.471 | 21.609 | |
calculate_gain_or_loss | 21.278 | 0.439 | 21.718 | |
calculate_logRatio_CNA | 20.616 | 0.377 | 20.994 | |
choose_cluster_scExp | 3.104 | 0.112 | 3.211 | |
colors_scExp | 0.266 | 0.001 | 0.267 | |
consensus_clustering_scExp | 2.740 | 0.085 | 2.811 | |
correlation_and_hierarchical_clust_scExp | 0.299 | 0.000 | 0.284 | |
create_project_folder | 0.000 | 0.001 | 0.001 | |
create_scDataset_raw | 5.362 | 0.222 | 5.584 | |
create_scExp | 0.447 | 0.000 | 0.447 | |
define_feature | 0.130 | 0.002 | 0.133 | |
detect_samples | 1.030 | 0.023 | 0.954 | |
differential_activation | 4.961 | 0.018 | 4.980 | |
differential_analysis_scExp | 2.704 | 0.002 | 2.706 | |
enrich_TF_ChEA3_genes | 0.458 | 0.019 | 1.649 | |
enrich_TF_ChEA3_scExp | 1.030 | 0.017 | 4.802 | |
exclude_features_scExp | 0.402 | 0.017 | 0.419 | |
feature_annotation_scExp | 1.286 | 0.049 | 1.334 | |
filter_correlated_cell_scExp | 9.194 | 0.118 | 9.298 | |
filter_scExp | 0.505 | 0.001 | 0.505 | |
find_clusters_louvain_scExp | 0.287 | 0.000 | 0.287 | |
find_top_features | 0.302 | 0.000 | 0.302 | |
gene_set_enrichment_analysis_scExp | 0.198 | 0.001 | 0.199 | |
generate_analysis | 0 | 0 | 0 | |
generate_coverage_tracks | 0 | 0 | 0 | |
generate_report | 0.001 | 0.000 | 0.000 | |
getExperimentNames | 0.219 | 0.001 | 0.221 | |
getMainExperiment | 0.252 | 0.001 | 0.254 | |
get_cyto_features | 17.980 | 0.147 | 18.128 | |
get_genomic_coordinates | 0.365 | 0.013 | 0.377 | |
get_most_variable_cyto | 22.000 | 0.236 | 22.237 | |
get_pathway_mat_scExp | 70.763 | 3.206 | 73.973 | |
has_genomic_coordinates | 0.601 | 0.015 | 0.617 | |
import_scExp | 7.040 | 0.050 | 7.092 | |
inter_correlation_scExp | 0.319 | 0.001 | 0.320 | |
intra_correlation_scExp | 0.337 | 0.001 | 0.337 | |
launchApp | 0.001 | 0.000 | 0.000 | |
normalize_scExp | 0.395 | 0.000 | 0.395 | |
num_cell_after_QC_filt_scExp | 0.402 | 0.001 | 0.403 | |
num_cell_after_cor_filt_scExp | 12.174 | 0.069 | 12.226 | |
num_cell_before_cor_filt_scExp | 0.204 | 0.000 | 0.204 | |
num_cell_in_cluster_scExp | 0.370 | 0.006 | 0.370 | |
num_cell_scExp | 0.326 | 0.000 | 0.326 | |
plot_cluster_consensus_scExp | 0.782 | 0.002 | 0.784 | |
plot_correlation_PCA_scExp | 0.956 | 0.000 | 0.955 | |
plot_coverage_BigWig | 0.197 | 0.000 | 0.197 | |
plot_differential_summary_scExp | 0.213 | 0.003 | 0.217 | |
plot_differential_volcano_scExp | 0.312 | 0.002 | 0.315 | |
plot_distribution_scExp | 0.389 | 0.001 | 0.390 | |
plot_gain_or_loss_barplots | 44.871 | 0.343 | 45.217 | |
plot_heatmap_scExp | 0.296 | 0.002 | 0.298 | |
plot_inter_correlation_scExp | 0.505 | 0.000 | 0.505 | |
plot_intra_correlation_scExp | 0.513 | 0.011 | 0.524 | |
plot_most_contributing_features | 0.381 | 0.002 | 0.383 | |
plot_percent_active_feature_scExp | 0.395 | 0.000 | 0.395 | |
plot_pie_most_contributing_chr | 0.278 | 0.002 | 0.280 | |
plot_reduced_dim_scExp | 1.210 | 0.009 | 1.219 | |
plot_reduced_dim_scExp_CNA | 22.388 | 0.112 | 22.501 | |
plot_top_TF_scExp | 0.453 | 0.001 | 0.454 | |
plot_violin_feature_scExp | 0.540 | 0.000 | 0.541 | |
preprocess_CPM | 0.372 | 0.005 | 0.378 | |
preprocess_RPKM | 0.398 | 0.014 | 0.412 | |
preprocess_TFIDF | 0.423 | 0.015 | 0.438 | |
preprocess_TPM | 0.396 | 0.002 | 0.399 | |
preprocess_feature_size_only | 0.365 | 0.005 | 0.370 | |
preprocessing_filtering_and_reduction | 8.896 | 0.073 | 8.963 | |
read_sparse_matrix | 0 | 0 | 0 | |
rebin_matrix | 6.673 | 0.090 | 20.650 | |
reduce_dims_scExp | 1.533 | 0.000 | 1.534 | |
scExp | 0.863 | 0.003 | 0.867 | |
subsample_scExp | 0.514 | 0.000 | 0.514 | |
subset_bam_call_peaks | 0.001 | 0.000 | 0.000 | |
summary_DA | 0.215 | 0.000 | 0.215 | |
swapAltExp_sameColData | 0.278 | 0.000 | 0.278 | |
table_enriched_genes_scExp | 0.195 | 0.000 | 0.195 | |
wrapper_Signac_FeatureMatrix | 0 | 0 | 0 | |