Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-09-22 12:06 -0400 (Mon, 22 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" | 4814 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4603 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4547 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4553 |
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 356/2333 | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: ChromSCape |
Version: 1.19.1 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:ChromSCape.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ChromSCape_1.19.1.tar.gz |
StartedAt: 2025-09-19 07:01:35 -0000 (Fri, 19 Sep 2025) |
EndedAt: 2025-09-19 07:18:16 -0000 (Fri, 19 Sep 2025) |
EllapsedTime: 1000.8 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: ChromSCape.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:ChromSCape.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ChromSCape_1.19.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/ChromSCape.Rcheck’ * using R version 4.5.0 (2025-04-11) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * 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: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’ * 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 92.788 1.599 94.745 plot_gain_or_loss_barplots 71.952 0.653 72.937 calculate_CNA 32.627 0.774 33.503 plot_reduced_dim_scExp_CNA 33.212 0.183 33.539 calculate_gain_or_loss 31.626 0.199 31.928 calculate_logRatio_CNA 31.518 0.224 31.844 calculate_cyto_mat 31.392 0.223 31.717 get_most_variable_cyto 31.184 0.227 31.566 get_cyto_features 28.339 0.219 28.744 num_cell_after_cor_filt_scExp 12.778 0.059 12.875 preprocessing_filtering_and_reduction 9.981 0.067 10.097 filter_correlated_cell_scExp 9.279 0.060 9.374 rebin_matrix 7.701 0.427 27.544 import_scExp 7.918 0.139 8.081 create_scDataset_raw 7.471 0.104 7.596 differential_activation 7.296 0.043 7.362 CompareWilcox 6.117 0.311 6.137 CompareedgeRGLM 6.032 0.188 6.235 enrich_TF_ChEA3_scExp 1.080 0.040 7.290 * 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 ‘/home/biocbuild/bbs-3.22-bioc/meat/ChromSCape.Rcheck/00check.log’ for details.
ChromSCape.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL ChromSCape ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘ChromSCape’ ... ** this is package ‘ChromSCape’ version ‘1.19.1’ ** using staged installation ** libs using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c RcppExports.cpp -o RcppExports.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c as_dist.cpp -o as_dist.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.5.0/lib -L/usr/local/lib -o ChromSCape.so RcppExports.o as_dist.o -L/home/biocbuild/R/R-4.5.0/lib -lR installing to /home/biocbuild/R/R-4.5.0/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 4.5.0 (2025-04-11) -- "How About a Twenty-Six" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: aarch64-unknown-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 42.191 3.444 45.557
ChromSCape.Rcheck/ChromSCape-Ex.timings
name | user | system | elapsed | |
CheA3_TF_nTargets | 0.007 | 0.000 | 0.008 | |
CompareWilcox | 6.117 | 0.311 | 6.137 | |
CompareedgeRGLM | 6.032 | 0.188 | 6.235 | |
annotToCol2 | 1.177 | 0.024 | 1.204 | |
calculate_CNA | 32.627 | 0.774 | 33.503 | |
calculate_cyto_mat | 31.392 | 0.223 | 31.717 | |
calculate_gain_or_loss | 31.626 | 0.199 | 31.928 | |
calculate_logRatio_CNA | 31.518 | 0.224 | 31.844 | |
choose_cluster_scExp | 4.231 | 0.087 | 4.332 | |
colors_scExp | 0.337 | 0.004 | 0.342 | |
consensus_clustering_scExp | 4.725 | 0.100 | 4.839 | |
correlation_and_hierarchical_clust_scExp | 0.430 | 0.008 | 0.440 | |
create_project_folder | 0.002 | 0.000 | 0.002 | |
create_scDataset_raw | 7.471 | 0.104 | 7.596 | |
create_scExp | 0.649 | 0.004 | 0.656 | |
define_feature | 0.17 | 0.00 | 0.17 | |
detect_samples | 1.952 | 0.000 | 1.847 | |
differential_activation | 7.296 | 0.043 | 7.362 | |
differential_analysis_scExp | 3.813 | 0.012 | 3.837 | |
enrich_TF_ChEA3_genes | 0.493 | 0.032 | 3.706 | |
enrich_TF_ChEA3_scExp | 1.08 | 0.04 | 7.29 | |
exclude_features_scExp | 0.632 | 0.000 | 0.634 | |
feature_annotation_scExp | 1.859 | 0.008 | 1.874 | |
filter_correlated_cell_scExp | 9.279 | 0.060 | 9.374 | |
filter_scExp | 0.779 | 0.004 | 0.786 | |
find_clusters_louvain_scExp | 0.380 | 0.004 | 0.386 | |
find_top_features | 0.388 | 0.004 | 0.393 | |
gene_set_enrichment_analysis_scExp | 0.214 | 0.000 | 0.214 | |
generate_analysis | 0 | 0 | 0 | |
generate_coverage_tracks | 0 | 0 | 0 | |
generate_report | 0 | 0 | 0 | |
getExperimentNames | 0.253 | 0.008 | 0.261 | |
getMainExperiment | 0.302 | 0.000 | 0.303 | |
get_cyto_features | 28.339 | 0.219 | 28.744 | |
get_genomic_coordinates | 0.557 | 0.008 | 0.567 | |
get_most_variable_cyto | 31.184 | 0.227 | 31.566 | |
get_pathway_mat_scExp | 92.788 | 1.599 | 94.745 | |
has_genomic_coordinates | 0.899 | 0.004 | 0.906 | |
import_scExp | 7.918 | 0.139 | 8.081 | |
inter_correlation_scExp | 0.412 | 0.000 | 0.416 | |
intra_correlation_scExp | 0.427 | 0.012 | 0.443 | |
launchApp | 0 | 0 | 0 | |
normalize_scExp | 0.582 | 0.008 | 0.595 | |
num_cell_after_QC_filt_scExp | 0.583 | 0.000 | 0.585 | |
num_cell_after_cor_filt_scExp | 12.778 | 0.059 | 12.875 | |
num_cell_before_cor_filt_scExp | 0.230 | 0.000 | 0.231 | |
num_cell_in_cluster_scExp | 0.49 | 0.00 | 0.49 | |
num_cell_scExp | 0.501 | 0.000 | 0.503 | |
plot_cluster_consensus_scExp | 1.454 | 0.008 | 1.467 | |
plot_correlation_PCA_scExp | 1.743 | 0.012 | 1.761 | |
plot_coverage_BigWig | 0.225 | 0.000 | 0.225 | |
plot_differential_summary_scExp | 0.243 | 0.004 | 0.248 | |
plot_differential_volcano_scExp | 0.336 | 0.000 | 0.337 | |
plot_distribution_scExp | 0.539 | 0.000 | 0.540 | |
plot_gain_or_loss_barplots | 71.952 | 0.653 | 72.937 | |
plot_heatmap_scExp | 0.371 | 0.000 | 0.372 | |
plot_inter_correlation_scExp | 0.885 | 0.004 | 0.892 | |
plot_intra_correlation_scExp | 0.887 | 0.004 | 0.894 | |
plot_most_contributing_features | 0.646 | 0.008 | 0.661 | |
plot_percent_active_feature_scExp | 0.716 | 0.000 | 0.718 | |
plot_pie_most_contributing_chr | 0.376 | 0.000 | 0.377 | |
plot_reduced_dim_scExp | 2.412 | 0.004 | 2.425 | |
plot_reduced_dim_scExp_CNA | 33.212 | 0.183 | 33.539 | |
plot_top_TF_scExp | 0.819 | 0.004 | 0.826 | |
plot_violin_feature_scExp | 0.868 | 0.007 | 0.881 | |
preprocess_CPM | 0.572 | 0.004 | 0.578 | |
preprocess_RPKM | 0.614 | 0.016 | 0.632 | |
preprocess_TFIDF | 0.611 | 0.020 | 0.634 | |
preprocess_TPM | 0.650 | 0.040 | 0.702 | |
preprocess_feature_size_only | 0.561 | 0.004 | 0.567 | |
preprocessing_filtering_and_reduction | 9.981 | 0.067 | 10.097 | |
read_sparse_matrix | 0 | 0 | 0 | |
rebin_matrix | 7.701 | 0.427 | 27.544 | |
reduce_dims_scExp | 2.122 | 0.084 | 2.213 | |
scExp | 1.435 | 0.088 | 1.527 | |
subsample_scExp | 0.853 | 0.048 | 0.904 | |
subset_bam_call_peaks | 0 | 0 | 0 | |
summary_DA | 0.261 | 0.000 | 0.262 | |
swapAltExp_sameColData | 0.349 | 0.019 | 0.371 | |
table_enriched_genes_scExp | 0.221 | 0.004 | 0.226 | |
wrapper_Signac_FeatureMatrix | 0 | 0 | 0 | |