Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-06-11 15:41 -0400 (Tue, 11 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4679 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
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 341/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ChromSCape 1.15.0 (landing page) Pacome Prompsy
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.4 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: 1.15.0 |
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_1.15.0.tar.gz |
StartedAt: 2024-06-10 01:16:20 -0400 (Mon, 10 Jun 2024) |
EndedAt: 2024-06-10 01:47:21 -0400 (Mon, 10 Jun 2024) |
EllapsedTime: 1861.3 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_1.15.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/ChromSCape.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * using platform: x86_64-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 Monterey 12.7.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ChromSCape/DESCRIPTION’ ... OK * this is package ‘ChromSCape’ version ‘1.15.0’ * 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 14.0.0 (clang-1400.0.29.202)’ * 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 120.116 0.832 142.670 get_pathway_mat_scExp 74.624 8.481 97.513 calculate_CNA 57.495 5.944 78.105 plot_reduced_dim_scExp_CNA 56.152 0.394 67.980 calculate_gain_or_loss 54.536 1.799 75.202 calculate_cyto_mat 53.534 2.255 74.917 calculate_logRatio_CNA 53.465 2.100 74.547 get_most_variable_cyto 54.743 0.678 69.225 get_cyto_features 49.886 0.591 65.646 num_cell_after_cor_filt_scExp 13.393 0.082 15.281 differential_activation 13.062 0.097 17.227 preprocessing_filtering_and_reduction 12.856 0.243 15.235 filter_correlated_cell_scExp 11.610 0.121 15.097 CompareedgeRGLM 10.811 0.795 13.090 create_scDataset_raw 8.768 0.698 12.594 import_scExp 8.417 0.565 10.409 CompareWilcox 7.908 0.754 8.785 rebin_matrix 7.602 0.092 45.859 plot_reduced_dim_scExp 7.426 0.080 9.064 choose_cluster_scExp 6.717 0.485 9.669 differential_analysis_scExp 6.748 0.040 8.654 consensus_clustering_scExp 5.892 0.536 8.599 plot_violin_feature_scExp 5.215 0.053 6.198 plot_percent_active_feature_scExp 5.190 0.054 6.651 feature_annotation_scExp 3.890 0.085 5.017 enrich_TF_ChEA3_scExp 1.955 0.093 6.920 enrich_TF_ChEA3_genes 0.971 0.407 9.066 * 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-x86_64/Resources/library’ * installing *source* package ‘ChromSCape’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-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 -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-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 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" Copyright (C) 2024 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 66.248 4.496 81.480
ChromSCape.Rcheck/ChromSCape-Ex.timings
name | user | system | elapsed | |
CheA3_TF_nTargets | 0.014 | 0.006 | 0.026 | |
CompareWilcox | 7.908 | 0.754 | 8.785 | |
CompareedgeRGLM | 10.811 | 0.795 | 13.090 | |
annotToCol2 | 1.874 | 0.070 | 2.175 | |
calculate_CNA | 57.495 | 5.944 | 78.105 | |
calculate_cyto_mat | 53.534 | 2.255 | 74.917 | |
calculate_gain_or_loss | 54.536 | 1.799 | 75.202 | |
calculate_logRatio_CNA | 53.465 | 2.100 | 74.547 | |
choose_cluster_scExp | 6.717 | 0.485 | 9.669 | |
colors_scExp | 0.637 | 0.012 | 0.890 | |
consensus_clustering_scExp | 5.892 | 0.536 | 8.599 | |
correlation_and_hierarchical_clust_scExp | 0.680 | 0.011 | 0.905 | |
create_project_folder | 0.003 | 0.004 | 0.009 | |
create_scDataset_raw | 8.768 | 0.698 | 12.594 | |
create_scExp | 1.497 | 0.039 | 2.081 | |
define_feature | 0.289 | 0.008 | 0.401 | |
detect_samples | 1.226 | 0.059 | 1.724 | |
differential_activation | 13.062 | 0.097 | 17.227 | |
differential_analysis_scExp | 6.748 | 0.040 | 8.654 | |
enrich_TF_ChEA3_genes | 0.971 | 0.407 | 9.066 | |
enrich_TF_ChEA3_scExp | 1.955 | 0.093 | 6.920 | |
exclude_features_scExp | 1.559 | 0.021 | 2.068 | |
feature_annotation_scExp | 3.890 | 0.085 | 5.017 | |
filter_correlated_cell_scExp | 11.610 | 0.121 | 15.097 | |
filter_scExp | 1.912 | 0.016 | 2.466 | |
find_clusters_louvain_scExp | 0.888 | 0.335 | 1.394 | |
find_top_features | 0.687 | 0.088 | 0.979 | |
gene_set_enrichment_analysis_scExp | 0.417 | 0.019 | 0.663 | |
generate_analysis | 0.000 | 0.001 | 0.002 | |
generate_coverage_tracks | 0.000 | 0.001 | 0.001 | |
generate_report | 0.001 | 0.001 | 0.001 | |
getExperimentNames | 0.489 | 0.022 | 0.672 | |
getMainExperiment | 0.595 | 0.035 | 0.816 | |
get_cyto_features | 49.886 | 0.591 | 65.646 | |
get_genomic_coordinates | 1.270 | 0.028 | 1.728 | |
get_most_variable_cyto | 54.743 | 0.678 | 69.225 | |
get_pathway_mat_scExp | 74.624 | 8.481 | 97.513 | |
has_genomic_coordinates | 2.178 | 0.022 | 2.411 | |
import_scExp | 8.417 | 0.565 | 10.409 | |
inter_correlation_scExp | 0.763 | 0.041 | 0.889 | |
intra_correlation_scExp | 0.807 | 0.033 | 0.929 | |
launchApp | 0.000 | 0.000 | 0.001 | |
normalize_scExp | 1.379 | 0.063 | 1.604 | |
num_cell_after_QC_filt_scExp | 1.511 | 0.077 | 1.754 | |
num_cell_after_cor_filt_scExp | 13.393 | 0.082 | 15.281 | |
num_cell_before_cor_filt_scExp | 0.458 | 0.018 | 0.542 | |
num_cell_in_cluster_scExp | 1.108 | 0.019 | 1.271 | |
num_cell_scExp | 1.218 | 0.009 | 1.351 | |
plot_cluster_consensus_scExp | 2.151 | 0.071 | 2.440 | |
plot_correlation_PCA_scExp | 2.503 | 0.036 | 2.914 | |
plot_coverage_BigWig | 0.456 | 0.014 | 0.587 | |
plot_differential_summary_scExp | 0.496 | 0.013 | 0.618 | |
plot_differential_volcano_scExp | 0.620 | 0.027 | 0.821 | |
plot_distribution_scExp | 1.005 | 0.040 | 1.177 | |
plot_gain_or_loss_barplots | 120.116 | 0.832 | 142.670 | |
plot_heatmap_scExp | 0.689 | 0.020 | 0.803 | |
plot_inter_correlation_scExp | 1.268 | 0.027 | 1.533 | |
plot_intra_correlation_scExp | 1.190 | 0.035 | 1.437 | |
plot_most_contributing_features | 0.896 | 0.020 | 1.181 | |
plot_percent_active_feature_scExp | 5.190 | 0.054 | 6.651 | |
plot_pie_most_contributing_chr | 0.620 | 0.018 | 0.784 | |
plot_reduced_dim_scExp | 7.426 | 0.080 | 9.064 | |
plot_reduced_dim_scExp_CNA | 56.152 | 0.394 | 67.980 | |
plot_top_TF_scExp | 1.108 | 0.027 | 1.337 | |
plot_violin_feature_scExp | 5.215 | 0.053 | 6.198 | |
preprocess_CPM | 1.385 | 0.074 | 1.778 | |
preprocess_RPKM | 1.365 | 0.061 | 1.749 | |
preprocess_TFIDF | 1.386 | 0.084 | 1.769 | |
preprocess_TPM | 1.379 | 0.064 | 1.689 | |
preprocess_feature_size_only | 1.341 | 0.067 | 1.632 | |
preprocessing_filtering_and_reduction | 12.856 | 0.243 | 15.235 | |
read_sparse_matrix | 0.000 | 0.001 | 0.003 | |
rebin_matrix | 7.602 | 0.092 | 45.859 | |
reduce_dims_scExp | 3.947 | 0.052 | 4.683 | |
scExp | 2.172 | 0.068 | 2.612 | |
subsample_scExp | 1.866 | 0.019 | 2.248 | |
subset_bam_call_peaks | 0.000 | 0.001 | 0.001 | |
summary_DA | 0.475 | 0.017 | 0.581 | |
swapAltExp_sameColData | 0.624 | 0.017 | 0.734 | |
table_enriched_genes_scExp | 0.411 | 0.016 | 0.535 | |
wrapper_Signac_FeatureMatrix | 0.001 | 0.001 | 0.001 | |