Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-05-31 05:44:31 -0000 (Wed, 31 May 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4219 |
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 |
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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
Package 334/2197 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ChromSCape 1.11.0 (landing page) Pacome Prompsy
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | WARNINGS | |||||||||
Package: ChromSCape |
Version: 1.11.0 |
Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:ChromSCape.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings ChromSCape_1.11.0.tar.gz |
StartedAt: 2023-05-30 03:25:46 -0000 (Tue, 30 May 2023) |
EndedAt: 2023-05-30 03:42:59 -0000 (Tue, 30 May 2023) |
EllapsedTime: 1033.5 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: ChromSCape.Rcheck |
Warnings: 4 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:ChromSCape.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings ChromSCape_1.11.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/ChromSCape.Rcheck’ * using R version 4.3.0 (2023-04-21) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.2 LTS * using session charset: UTF-8 * checking for file ‘ChromSCape/DESCRIPTION’ ... OK * this is package ‘ChromSCape’ version ‘1.11.0’ * 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: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0’ * checking installed package size ... NOTE installed size is 5.4Mb sub-directories of 1Mb or more: data 1.5Mb 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 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 loading without being on the library search path ... OK * checking 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 documentation object 'generate_analysis': 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 documentation object 'rebin_matrix' ‘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 68.471 4.736 73.212 get_pathway_mat_scExp 57.887 1.472 59.359 calculate_CNA 32.742 1.900 34.642 plot_reduced_dim_scExp_CNA 31.315 0.796 32.114 calculate_gain_or_loss 30.718 0.563 31.281 calculate_cyto_mat 30.389 0.764 31.153 get_most_variable_cyto 29.911 0.756 30.668 calculate_logRatio_CNA 29.960 0.444 30.405 get_cyto_features 27.742 0.784 28.528 num_cell_after_cor_filt_scExp 13.386 0.991 14.262 filter_correlated_cell_scExp 12.155 1.287 13.369 create_scDataset_raw 11.276 0.308 11.584 preprocessing_filtering_and_reduction 10.585 0.136 10.722 differential_activation 8.175 0.088 8.264 import_scExp 8.081 0.120 8.201 rebin_matrix 7.553 0.090 27.169 CompareWilcox 6.858 0.545 6.846 CompareedgeRGLM 6.632 0.248 6.879 enrich_TF_ChEA3_scExp 1.403 0.116 7.595 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘vignette.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 4 WARNINGs, 5 NOTEs See ‘/home/biocbuild/bbs-3.18-bioc/meat/ChromSCape.Rcheck/00check.log’ for details.
ChromSCape.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL ChromSCape ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’ * installing *source* package ‘ChromSCape’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0’ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c as_dist.cpp -o as_dist.o g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.3.0/lib -L/usr/local/lib -o ChromSCape.so RcppExports.o as_dist.o -L/home/biocbuild/R/R-4.3.0/lib -lR installing to /home/biocbuild/R/R-4.3.0/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 4.3.0 (2023-04-21) -- "Already Tomorrow" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu (64-bit) 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 55.728 3.047 58.518
ChromSCape.Rcheck/ChromSCape-Ex.timings
name | user | system | elapsed | |
CheA3_TF_nTargets | 0.011 | 0.000 | 0.010 | |
CompareWilcox | 6.858 | 0.545 | 6.846 | |
CompareedgeRGLM | 6.632 | 0.248 | 6.879 | |
annotToCol2 | 1.187 | 0.080 | 1.267 | |
calculate_CNA | 32.742 | 1.900 | 34.642 | |
calculate_cyto_mat | 30.389 | 0.764 | 31.153 | |
calculate_gain_or_loss | 30.718 | 0.563 | 31.281 | |
calculate_logRatio_CNA | 29.960 | 0.444 | 30.405 | |
choose_cluster_scExp | 4.809 | 0.108 | 4.917 | |
colors_scExp | 0.368 | 0.000 | 0.368 | |
consensus_clustering_scExp | 4.344 | 0.080 | 4.424 | |
correlation_and_hierarchical_clust_scExp | 0.38 | 0.00 | 0.38 | |
create_project_folder | 0.002 | 0.000 | 0.002 | |
create_scDataset_raw | 11.276 | 0.308 | 11.584 | |
create_scExp | 0.906 | 0.004 | 0.910 | |
define_feature | 0.219 | 0.004 | 0.223 | |
detect_samples | 2.229 | 0.004 | 2.154 | |
differential_activation | 8.175 | 0.088 | 8.264 | |
differential_analysis_scExp | 4.278 | 0.052 | 4.331 | |
enrich_TF_ChEA3_genes | 0.593 | 0.080 | 3.789 | |
enrich_TF_ChEA3_scExp | 1.403 | 0.116 | 7.595 | |
exclude_features_scExp | 0.986 | 0.044 | 1.031 | |
feature_annotation_scExp | 2.497 | 0.132 | 2.629 | |
filter_correlated_cell_scExp | 12.155 | 1.287 | 13.369 | |
filter_scExp | 1.231 | 0.048 | 1.279 | |
find_clusters_louvain_scExp | 0.526 | 0.517 | 0.704 | |
find_top_features | 0.419 | 0.056 | 0.475 | |
gene_set_enrichment_analysis_scExp | 0.272 | 0.016 | 0.288 | |
generate_analysis | 0 | 0 | 0 | |
generate_coverage_tracks | 0 | 0 | 0 | |
generate_report | 0.001 | 0.000 | 0.000 | |
getExperimentNames | 0.317 | 0.016 | 0.333 | |
getMainExperiment | 0.367 | 0.016 | 0.383 | |
get_cyto_features | 27.742 | 0.784 | 28.528 | |
get_genomic_coordinates | 0.797 | 0.052 | 0.848 | |
get_most_variable_cyto | 29.911 | 0.756 | 30.668 | |
get_pathway_mat_scExp | 57.887 | 1.472 | 59.359 | |
has_genomic_coordinates | 1.401 | 0.008 | 1.409 | |
import_scExp | 8.081 | 0.120 | 8.201 | |
inter_correlation_scExp | 0.487 | 0.008 | 0.495 | |
intra_correlation_scExp | 0.452 | 0.004 | 0.456 | |
launchApp | 0 | 0 | 0 | |
normalize_scExp | 0.797 | 0.012 | 0.809 | |
num_cell_after_QC_filt_scExp | 0.893 | 0.036 | 0.929 | |
num_cell_after_cor_filt_scExp | 13.386 | 0.991 | 14.262 | |
num_cell_before_cor_filt_scExp | 0.267 | 0.012 | 0.279 | |
num_cell_in_cluster_scExp | 0.632 | 0.016 | 0.647 | |
num_cell_scExp | 0.769 | 0.031 | 0.801 | |
plot_cluster_consensus_scExp | 1.318 | 0.076 | 1.394 | |
plot_correlation_PCA_scExp | 1.249 | 0.012 | 1.261 | |
plot_coverage_BigWig | 0.269 | 0.000 | 0.269 | |
plot_differential_summary_scExp | 0.292 | 0.012 | 0.304 | |
plot_differential_volcano_scExp | 0.374 | 0.008 | 0.382 | |
plot_distribution_scExp | 0.537 | 0.016 | 0.553 | |
plot_gain_or_loss_barplots | 68.471 | 4.736 | 73.212 | |
plot_heatmap_scExp | 0.375 | 0.004 | 0.380 | |
plot_inter_correlation_scExp | 0.693 | 0.008 | 0.701 | |
plot_intra_correlation_scExp | 0.694 | 0.000 | 0.694 | |
plot_most_contributing_features | 0.511 | 0.004 | 0.515 | |
plot_percent_active_feature_scExp | 2.820 | 0.048 | 2.868 | |
plot_pie_most_contributing_chr | 0.341 | 0.004 | 0.345 | |
plot_reduced_dim_scExp | 4.190 | 0.056 | 4.246 | |
plot_reduced_dim_scExp_CNA | 31.315 | 0.796 | 32.114 | |
plot_top_TF_scExp | 0.569 | 0.011 | 0.580 | |
plot_violin_feature_scExp | 2.936 | 0.060 | 2.996 | |
preprocess_CPM | 0.835 | 0.032 | 0.866 | |
preprocess_RPKM | 0.815 | 0.036 | 0.851 | |
preprocess_TFIDF | 0.803 | 0.024 | 0.827 | |
preprocess_TPM | 0.816 | 0.076 | 0.892 | |
preprocess_feature_size_only | 0.770 | 0.024 | 0.794 | |
preprocessing_filtering_and_reduction | 10.585 | 0.136 | 10.722 | |
read_sparse_matrix | 0.001 | 0.000 | 0.000 | |
rebin_matrix | 7.553 | 0.090 | 27.169 | |
reduce_dims_scExp | 2.483 | 0.028 | 2.511 | |
scExp | 1.330 | 0.112 | 1.441 | |
subsample_scExp | 1.128 | 0.060 | 1.188 | |
subset_bam_call_peaks | 0 | 0 | 0 | |
summary_DA | 0.268 | 0.004 | 0.273 | |
swapAltExp_sameColData | 0.364 | 0.008 | 0.371 | |
table_enriched_genes_scExp | 0.237 | 0.008 | 0.244 | |
wrapper_Signac_FeatureMatrix | 0 | 0 | 0 | |