Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 348/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ChromSCape 1.16.0 (landing page) Pacome Prompsy
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 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: 1.16.0 |
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_1.16.0.tar.gz |
StartedAt: 2024-12-20 14:30:26 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 14:45:27 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 901.4 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: ChromSCape.Rcheck |
Warnings: 3 |
############################################################################## ############################################################################## ### ### 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_1.16.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/ChromSCape.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ChromSCape/DESCRIPTION’ ... OK * this is package ‘ChromSCape’ version ‘1.16.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * 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 15.0.0 (clang-1500.0.40.1)’ * used SDK: ‘MacOSX11.3.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 'library' or 'require' call not declared from: ‘dplyr’ 'library' or 'require' call to ‘dplyr’ in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. * 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 ... NOTE prepare_Rd: raw_counts_to_sparse_matrix.Rd:6-8: Dropping empty section \source * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... WARNING Codoc mismatches from Rd file 'generate_analysis.Rd': generate_analysis Code: function(input_data_folder, analysis_name = "Analysis_1", output_directory = "./", input_data_type = c("scBED", "DenseMatrix", "SparseMatrix", "scBAM")[1], feature_count_on = c("bins", "genebody", "peaks")[1], feature_count_parameter = 50000, rebin_sparse_matrix = FALSE, ref_genome = c("hg38", "mm10")[1], run = c("filter", "CNA", "cluster", "consensus", "coverage", "DA", "GSA", "report")[c(1, 3, 5, 6, 7, 8)], min_reads_per_cell = 1000, max_quantile_read_per_cell = 99, n_top_features = 40000, norm_type = "CPM", subsample_n = NULL, exclude_regions = NULL, n_clust = NULL, corr_threshold = 99, percent_correlation = 1, maxK = 10, qval.th = 0.1, logFC.th = 1, enrichment_qval = 0.1, doBatchCorr = FALSE, batch_sels = NULL, control_samples_CNA = NULL, genes_to_plot = c("Krt8", "Krt5", "Tgfb1", "Foxq1", "Cdkn2b", "Cdkn2a", "chr7:15000000-20000000")) Docs: function(input_data_folder, analysis_name = "Analysis_1", output_directory = "./", input_data_type = c("scBED", "DenseMatrix", "SparseMatrix", "scBAM")[1], rebin_sparse_matrix = FALSE, feature_count_on = c("bins", "genebody", "peaks")[1], feature_count_parameter = 50000, ref_genome = c("hg38", "mm10")[1], run = c("filter", "CNA", "cluster", "consensus", "peak_call", "coverage", "DA", "GSA", "report")[c(1, 3, 6, 7, 8, 9)], min_reads_per_cell = 1000, max_quantile_read_per_cell = 99, n_top_features = 40000, norm_type = "CPM", subsample_n = NULL, exclude_regions = NULL, n_clust = NULL, corr_threshold = 99, percent_correlation = 1, maxK = 10, qval.th = 0.1, logFC.th = 1, enrichment_qval = 0.1, doBatchCorr = FALSE, batch_sels = NULL, control_samples_CNA = NULL, genes_to_plot = c("Krt8", "Krt5", "Tgfb1", "Foxq1", "Cdkn2b", "Cdkn2a", "chr7:15000000-20000000")) Mismatches in argument names: Position: 5 Code: feature_count_on Docs: rebin_sparse_matrix Position: 6 Code: feature_count_parameter Docs: feature_count_on Position: 7 Code: rebin_sparse_matrix Docs: feature_count_parameter Mismatches in argument default values: Name: 'run' Code: c("filter", "CNA", "cluster", "consensus", "coverage", "DA", "GSA", "report")[c(1, 3, 5, 6, 7, 8)] Docs: c("filter", "CNA", "cluster", "consensus", "peak_call", "coverage", "DA", "GSA", "report")[c(1, 3, 6, 7, 8, 9)] * checking Rd \usage sections ... WARNING Undocumented arguments in Rd file 'rebin_matrix.Rd' ‘rebin_function’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 plot_gain_or_loss_barplots 53.518 0.432 54.205 get_pathway_mat_scExp 44.122 4.391 48.793 plot_reduced_dim_scExp_CNA 27.152 0.205 27.463 calculate_CNA 25.833 1.387 27.388 calculate_cyto_mat 25.928 0.672 26.739 calculate_gain_or_loss 25.303 0.575 25.999 calculate_logRatio_CNA 25.064 0.730 25.928 get_most_variable_cyto 25.106 0.157 25.350 get_cyto_features 22.181 0.118 22.381 num_cell_after_cor_filt_scExp 14.538 0.077 14.655 filter_correlated_cell_scExp 13.891 0.086 14.228 preprocessing_filtering_and_reduction 11.111 0.189 11.327 create_scDataset_raw 8.945 0.638 9.666 import_scExp 9.099 0.370 9.509 rebin_matrix 9.002 0.078 27.689 CompareWilcox 7.659 0.532 7.733 differential_activation 5.999 0.046 6.110 CompareedgeRGLM 5.040 0.312 5.369 enrich_TF_ChEA3_scExp 1.155 0.097 5.571 * 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: 3 WARNINGs, 4 NOTEs See ‘/Users/biocbuild/bbs-3.20-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/4.4-arm64/Resources/library’ * installing *source* package ‘ChromSCape’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/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++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/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++17 -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 -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/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 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-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 48.664 2.992 52.448
ChromSCape.Rcheck/ChromSCape-Ex.timings
name | user | system | elapsed | |
CheA3_TF_nTargets | 0.011 | 0.003 | 0.015 | |
CompareWilcox | 7.659 | 0.532 | 7.733 | |
CompareedgeRGLM | 5.040 | 0.312 | 5.369 | |
annotToCol2 | 2.300 | 0.291 | 2.637 | |
calculate_CNA | 25.833 | 1.387 | 27.388 | |
calculate_cyto_mat | 25.928 | 0.672 | 26.739 | |
calculate_gain_or_loss | 25.303 | 0.575 | 25.999 | |
calculate_logRatio_CNA | 25.064 | 0.730 | 25.928 | |
choose_cluster_scExp | 4.159 | 0.540 | 4.734 | |
colors_scExp | 0.415 | 0.012 | 0.429 | |
consensus_clustering_scExp | 3.845 | 0.531 | 4.433 | |
correlation_and_hierarchical_clust_scExp | 0.428 | 0.014 | 0.443 | |
create_project_folder | 0.002 | 0.002 | 0.004 | |
create_scDataset_raw | 8.945 | 0.638 | 9.666 | |
create_scExp | 0.413 | 0.029 | 0.467 | |
define_feature | 0.192 | 0.016 | 0.211 | |
detect_samples | 1.821 | 0.047 | 1.904 | |
differential_activation | 5.999 | 0.046 | 6.110 | |
differential_analysis_scExp | 3.281 | 0.027 | 3.320 | |
enrich_TF_ChEA3_genes | 0.542 | 0.112 | 2.419 | |
enrich_TF_ChEA3_scExp | 1.155 | 0.097 | 5.571 | |
exclude_features_scExp | 0.504 | 0.020 | 0.533 | |
feature_annotation_scExp | 1.701 | 0.080 | 1.793 | |
filter_correlated_cell_scExp | 13.891 | 0.086 | 14.228 | |
filter_scExp | 0.584 | 0.020 | 0.613 | |
find_clusters_louvain_scExp | 0.453 | 0.011 | 0.464 | |
find_top_features | 0.483 | 0.016 | 0.511 | |
gene_set_enrichment_analysis_scExp | 0.335 | 0.010 | 0.347 | |
generate_analysis | 0.000 | 0.001 | 0.000 | |
generate_coverage_tracks | 0 | 0 | 0 | |
generate_report | 0.000 | 0.001 | 0.000 | |
getExperimentNames | 0.371 | 0.013 | 0.385 | |
getMainExperiment | 0.421 | 0.012 | 0.434 | |
get_cyto_features | 22.181 | 0.118 | 22.381 | |
get_genomic_coordinates | 0.415 | 0.014 | 0.429 | |
get_most_variable_cyto | 25.106 | 0.157 | 25.350 | |
get_pathway_mat_scExp | 44.122 | 4.391 | 48.793 | |
has_genomic_coordinates | 0.739 | 0.031 | 0.772 | |
import_scExp | 9.099 | 0.370 | 9.509 | |
inter_correlation_scExp | 0.489 | 0.027 | 0.517 | |
intra_correlation_scExp | 0.528 | 0.021 | 0.551 | |
launchApp | 0 | 0 | 0 | |
normalize_scExp | 0.467 | 0.043 | 0.512 | |
num_cell_after_QC_filt_scExp | 0.479 | 0.014 | 0.494 | |
num_cell_after_cor_filt_scExp | 14.538 | 0.077 | 14.655 | |
num_cell_before_cor_filt_scExp | 0.332 | 0.010 | 0.343 | |
num_cell_in_cluster_scExp | 0.541 | 0.010 | 0.554 | |
num_cell_scExp | 0.390 | 0.018 | 0.408 | |
plot_cluster_consensus_scExp | 1.022 | 0.043 | 1.066 | |
plot_correlation_PCA_scExp | 1.192 | 0.034 | 1.229 | |
plot_coverage_BigWig | 0.320 | 0.015 | 0.336 | |
plot_differential_summary_scExp | 0.351 | 0.007 | 0.359 | |
plot_differential_volcano_scExp | 0.447 | 0.014 | 0.461 | |
plot_distribution_scExp | 0.574 | 0.014 | 0.595 | |
plot_gain_or_loss_barplots | 53.518 | 0.432 | 54.205 | |
plot_heatmap_scExp | 0.449 | 0.022 | 0.472 | |
plot_inter_correlation_scExp | 0.683 | 0.015 | 0.700 | |
plot_intra_correlation_scExp | 0.625 | 0.016 | 0.643 | |
plot_most_contributing_features | 0.615 | 0.025 | 0.643 | |
plot_percent_active_feature_scExp | 1.809 | 0.051 | 1.861 | |
plot_pie_most_contributing_chr | 0.455 | 0.018 | 0.475 | |
plot_reduced_dim_scExp | 2.829 | 0.042 | 2.886 | |
plot_reduced_dim_scExp_CNA | 27.152 | 0.205 | 27.463 | |
plot_top_TF_scExp | 0.593 | 0.020 | 0.614 | |
plot_violin_feature_scExp | 2.014 | 0.047 | 2.080 | |
preprocess_CPM | 0.464 | 0.037 | 0.504 | |
preprocess_RPKM | 0.520 | 0.055 | 0.579 | |
preprocess_TFIDF | 0.453 | 0.030 | 0.487 | |
preprocess_TPM | 0.479 | 0.032 | 0.513 | |
preprocess_feature_size_only | 0.440 | 0.041 | 0.486 | |
preprocessing_filtering_and_reduction | 11.111 | 0.189 | 11.327 | |
read_sparse_matrix | 0.000 | 0.001 | 0.001 | |
rebin_matrix | 9.002 | 0.078 | 27.689 | |
reduce_dims_scExp | 1.862 | 0.038 | 1.926 | |
scExp | 1.148 | 0.038 | 1.194 | |
subsample_scExp | 0.623 | 0.022 | 0.657 | |
subset_bam_call_peaks | 0 | 0 | 0 | |
summary_DA | 0.350 | 0.013 | 0.367 | |
swapAltExp_sameColData | 0.423 | 0.013 | 0.437 | |
table_enriched_genes_scExp | 0.322 | 0.014 | 0.351 | |
wrapper_Signac_FeatureMatrix | 0.000 | 0.000 | 0.001 | |