Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-03-04 11:38:59 -0500 (Mon, 04 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4676 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" | 4414 |
merida1 | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4441 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" | 4417 |
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 344/2251 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ChromSCape 1.13.0 (landing page) Pacome Prompsy
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / 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: 1.13.0 |
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_1.13.0.tar.gz |
StartedAt: 2024-03-02 01:39:24 -0500 (Sat, 02 Mar 2024) |
EndedAt: 2024-03-02 02:08:38 -0500 (Sat, 02 Mar 2024) |
EllapsedTime: 1754.2 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: ChromSCape.Rcheck |
Warnings: 4 |
############################################################################## ############################################################################## ### ### 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_1.13.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/ChromSCape.Rcheck’ * using R Under development (unstable) (2024-01-16 r85808) * 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 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ChromSCape/DESCRIPTION’ ... OK * this is package ‘ChromSCape’ version ‘1.13.0’ * 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 R 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 ... WARNING Found the following significant warnings: Warning: 'as(<matrix>, "dspMatrix")' is deprecated. Deprecated functions may be defunct as soon as of the next release of R. See ?Deprecated. Examples with CPU (user + system) or elapsed time > 5s user system elapsed plot_gain_or_loss_barplots 110.549 1.052 136.078 get_pathway_mat_scExp 63.614 8.767 85.023 calculate_CNA 53.422 4.501 68.391 calculate_gain_or_loss 51.348 1.986 64.581 plot_reduced_dim_scExp_CNA 52.143 0.542 62.265 calculate_cyto_mat 50.280 2.232 62.010 get_most_variable_cyto 51.562 0.944 64.618 calculate_logRatio_CNA 49.889 2.158 60.917 get_cyto_features 48.279 1.213 66.346 differential_activation 12.477 0.208 16.081 num_cell_after_cor_filt_scExp 12.281 0.140 15.004 preprocessing_filtering_and_reduction 11.777 0.246 14.323 filter_correlated_cell_scExp 11.471 0.151 14.277 CompareedgeRGLM 10.540 0.770 13.485 create_scDataset_raw 8.422 0.841 11.403 import_scExp 7.737 0.707 10.512 CompareWilcox 7.477 0.804 8.601 rebin_matrix 7.082 0.111 43.936 plot_reduced_dim_scExp 6.757 0.069 8.167 choose_cluster_scExp 5.993 0.599 14.945 differential_analysis_scExp 6.484 0.084 7.903 consensus_clustering_scExp 5.612 0.532 7.216 plot_violin_feature_scExp 5.133 0.073 6.212 plot_percent_active_feature_scExp 4.838 0.062 6.004 enrich_TF_ChEA3_scExp 1.895 0.097 5.462 * 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: 4 WARNINGs, 4 NOTEs See ‘/Users/biocbuild/bbs-3.19-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 Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 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 63.678 4.755 81.082
ChromSCape.Rcheck/ChromSCape-Ex.timings
name | user | system | elapsed | |
CheA3_TF_nTargets | 0.014 | 0.006 | 0.023 | |
CompareWilcox | 7.477 | 0.804 | 8.601 | |
CompareedgeRGLM | 10.540 | 0.770 | 13.485 | |
annotToCol2 | 1.907 | 0.074 | 2.352 | |
calculate_CNA | 53.422 | 4.501 | 68.391 | |
calculate_cyto_mat | 50.280 | 2.232 | 62.010 | |
calculate_gain_or_loss | 51.348 | 1.986 | 64.581 | |
calculate_logRatio_CNA | 49.889 | 2.158 | 60.917 | |
choose_cluster_scExp | 5.993 | 0.599 | 14.945 | |
colors_scExp | 0.590 | 0.025 | 0.742 | |
consensus_clustering_scExp | 5.612 | 0.532 | 7.216 | |
correlation_and_hierarchical_clust_scExp | 0.609 | 0.013 | 0.710 | |
create_project_folder | 0.002 | 0.004 | 0.007 | |
create_scDataset_raw | 8.422 | 0.841 | 11.403 | |
create_scExp | 1.415 | 0.027 | 1.861 | |
define_feature | 0.302 | 0.035 | 0.437 | |
detect_samples | 1.205 | 0.083 | 1.603 | |
differential_activation | 12.477 | 0.208 | 16.081 | |
differential_analysis_scExp | 6.484 | 0.084 | 7.903 | |
enrich_TF_ChEA3_genes | 0.948 | 0.415 | 2.590 | |
enrich_TF_ChEA3_scExp | 1.895 | 0.097 | 5.462 | |
exclude_features_scExp | 1.493 | 0.019 | 1.908 | |
feature_annotation_scExp | 3.715 | 0.097 | 4.664 | |
filter_correlated_cell_scExp | 11.471 | 0.151 | 14.277 | |
filter_scExp | 1.846 | 0.020 | 2.306 | |
find_clusters_louvain_scExp | 0.851 | 0.404 | 1.310 | |
find_top_features | 0.660 | 0.077 | 0.933 | |
gene_set_enrichment_analysis_scExp | 0.431 | 0.028 | 0.615 | |
generate_analysis | 0.001 | 0.001 | 0.001 | |
generate_coverage_tracks | 0.000 | 0.001 | 0.001 | |
generate_report | 0.000 | 0.001 | 0.001 | |
getExperimentNames | 0.472 | 0.025 | 0.606 | |
getMainExperiment | 0.551 | 0.032 | 0.692 | |
get_cyto_features | 48.279 | 1.213 | 66.346 | |
get_genomic_coordinates | 1.285 | 0.056 | 1.913 | |
get_most_variable_cyto | 51.562 | 0.944 | 64.618 | |
get_pathway_mat_scExp | 63.614 | 8.767 | 85.023 | |
has_genomic_coordinates | 2.077 | 0.029 | 2.669 | |
import_scExp | 7.737 | 0.707 | 10.512 | |
inter_correlation_scExp | 0.771 | 0.042 | 1.015 | |
intra_correlation_scExp | 0.709 | 0.039 | 1.364 | |
launchApp | 0.000 | 0.001 | 0.000 | |
normalize_scExp | 1.063 | 0.077 | 1.285 | |
num_cell_after_QC_filt_scExp | 1.447 | 0.110 | 1.925 | |
num_cell_after_cor_filt_scExp | 12.281 | 0.140 | 15.004 | |
num_cell_before_cor_filt_scExp | 0.406 | 0.017 | 0.526 | |
num_cell_in_cluster_scExp | 0.998 | 0.017 | 1.229 | |
num_cell_scExp | 1.145 | 0.016 | 1.461 | |
plot_cluster_consensus_scExp | 2.249 | 0.091 | 2.936 | |
plot_correlation_PCA_scExp | 2.760 | 0.043 | 3.534 | |
plot_coverage_BigWig | 0.445 | 0.013 | 0.566 | |
plot_differential_summary_scExp | 0.485 | 0.019 | 0.608 | |
plot_differential_volcano_scExp | 0.611 | 0.024 | 0.805 | |
plot_distribution_scExp | 0.917 | 0.023 | 1.120 | |
plot_gain_or_loss_barplots | 110.549 | 1.052 | 136.078 | |
plot_heatmap_scExp | 0.598 | 0.021 | 0.761 | |
plot_inter_correlation_scExp | 1.249 | 0.029 | 1.581 | |
plot_intra_correlation_scExp | 1.249 | 0.019 | 1.603 | |
plot_most_contributing_features | 0.898 | 0.023 | 1.149 | |
plot_percent_active_feature_scExp | 4.838 | 0.062 | 6.004 | |
plot_pie_most_contributing_chr | 0.560 | 0.020 | 0.722 | |
plot_reduced_dim_scExp | 6.757 | 0.069 | 8.167 | |
plot_reduced_dim_scExp_CNA | 52.143 | 0.542 | 62.265 | |
plot_top_TF_scExp | 1.101 | 0.032 | 1.453 | |
plot_violin_feature_scExp | 5.133 | 0.073 | 6.212 | |
preprocess_CPM | 1.286 | 0.080 | 1.663 | |
preprocess_RPKM | 1.293 | 0.072 | 1.702 | |
preprocess_TFIDF | 1.313 | 0.107 | 1.743 | |
preprocess_TPM | 1.323 | 0.072 | 1.612 | |
preprocess_feature_size_only | 1.296 | 0.120 | 1.662 | |
preprocessing_filtering_and_reduction | 11.777 | 0.246 | 14.323 | |
read_sparse_matrix | 0.000 | 0.001 | 0.001 | |
rebin_matrix | 7.082 | 0.111 | 43.936 | |
reduce_dims_scExp | 3.818 | 0.069 | 4.885 | |
scExp | 2.058 | 0.063 | 2.642 | |
subsample_scExp | 1.758 | 0.023 | 2.121 | |
subset_bam_call_peaks | 0.000 | 0.001 | 0.002 | |
summary_DA | 0.434 | 0.018 | 0.537 | |
swapAltExp_sameColData | 0.596 | 0.014 | 0.699 | |
table_enriched_genes_scExp | 0.387 | 0.013 | 0.464 | |
wrapper_Signac_FeatureMatrix | 0.000 | 0.001 | 0.001 | |