Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-06-14 14:37 -0400 (Fri, 14 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4757 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4491 |
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 348/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ChromSCape 1.14.0 (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 | |||||||||
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: 1.14.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:ChromSCape.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings ChromSCape_1.14.0.tar.gz |
StartedAt: 2024-06-12 21:35:40 -0400 (Wed, 12 Jun 2024) |
EndedAt: 2024-06-12 21:48:10 -0400 (Wed, 12 Jun 2024) |
EllapsedTime: 749.6 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: ChromSCape.Rcheck |
Warnings: 3 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:ChromSCape.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings ChromSCape_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/ChromSCape.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘ChromSCape/DESCRIPTION’ ... OK * this is package ‘ChromSCape’ version ‘1.14.0’ * 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 11.4.0-1ubuntu1~22.04) 11.4.0’ * 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 loading without being on the library search path ... 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 44.836 0.184 45.020 get_pathway_mat_scExp 30.971 1.560 32.534 calculate_CNA 23.560 2.513 26.079 calculate_cyto_mat 21.842 0.968 22.852 plot_reduced_dim_scExp_CNA 21.956 0.136 22.092 calculate_logRatio_CNA 20.858 0.763 21.623 calculate_gain_or_loss 20.563 0.752 21.316 get_most_variable_cyto 19.830 0.280 20.111 get_cyto_features 18.089 0.164 18.256 num_cell_after_cor_filt_scExp 12.323 0.156 12.467 filter_correlated_cell_scExp 9.983 0.104 10.075 preprocessing_filtering_and_reduction 8.819 0.004 8.815 rebin_matrix 7.034 0.700 21.752 import_scExp 7.460 0.068 7.535 create_scDataset_raw 6.586 0.380 6.966 CompareWilcox 6.289 0.266 6.495 differential_activation 5.128 0.052 5.179 CompareedgeRGLM 4.786 0.270 4.861 enrich_TF_ChEA3_scExp 0.981 0.027 5.082 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 3 WARNINGs, 4 NOTEs See ‘/home/biocbuild/bbs-3.19-bioc/meat/ChromSCape.Rcheck/00check.log’ for details.
ChromSCape.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL ChromSCape ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘ChromSCape’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c as_dist.cpp -o as_dist.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o ChromSCape.so RcppExports.o as_dist.o -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.19-bioc/R/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 4.4.0 (2024-04-24) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-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 41.120 2.019 43.076
ChromSCape.Rcheck/ChromSCape-Ex.timings
name | user | system | elapsed | |
CheA3_TF_nTargets | 0.009 | 0.000 | 0.009 | |
CompareWilcox | 6.289 | 0.266 | 6.495 | |
CompareedgeRGLM | 4.786 | 0.270 | 4.861 | |
annotToCol2 | 0.893 | 0.051 | 0.944 | |
calculate_CNA | 23.560 | 2.513 | 26.079 | |
calculate_cyto_mat | 21.842 | 0.968 | 22.852 | |
calculate_gain_or_loss | 20.563 | 0.752 | 21.316 | |
calculate_logRatio_CNA | 20.858 | 0.763 | 21.623 | |
choose_cluster_scExp | 3.604 | 0.113 | 3.716 | |
colors_scExp | 0.291 | 0.000 | 0.291 | |
consensus_clustering_scExp | 2.964 | 0.112 | 3.071 | |
correlation_and_hierarchical_clust_scExp | 0.308 | 0.004 | 0.306 | |
create_project_folder | 0.001 | 0.000 | 0.002 | |
create_scDataset_raw | 6.586 | 0.380 | 6.966 | |
create_scExp | 0.584 | 0.000 | 0.584 | |
define_feature | 0.134 | 0.004 | 0.138 | |
detect_samples | 0.957 | 0.016 | 0.917 | |
differential_activation | 5.128 | 0.052 | 5.179 | |
differential_analysis_scExp | 2.681 | 0.040 | 2.720 | |
enrich_TF_ChEA3_genes | 0.437 | 0.096 | 1.737 | |
enrich_TF_ChEA3_scExp | 0.981 | 0.027 | 5.082 | |
exclude_features_scExp | 0.581 | 0.004 | 0.585 | |
feature_annotation_scExp | 1.534 | 0.048 | 1.582 | |
filter_correlated_cell_scExp | 9.983 | 0.104 | 10.075 | |
filter_scExp | 0.741 | 0.000 | 0.741 | |
find_clusters_louvain_scExp | 0.401 | 0.510 | 0.533 | |
find_top_features | 0.327 | 0.012 | 0.339 | |
gene_set_enrichment_analysis_scExp | 0.21 | 0.00 | 0.21 | |
generate_analysis | 0 | 0 | 0 | |
generate_coverage_tracks | 0 | 0 | 0 | |
generate_report | 0 | 0 | 0 | |
getExperimentNames | 0.237 | 0.004 | 0.242 | |
getMainExperiment | 0.278 | 0.000 | 0.278 | |
get_cyto_features | 18.089 | 0.164 | 18.256 | |
get_genomic_coordinates | 0.501 | 0.004 | 0.505 | |
get_most_variable_cyto | 19.830 | 0.280 | 20.111 | |
get_pathway_mat_scExp | 30.971 | 1.560 | 32.534 | |
has_genomic_coordinates | 0.847 | 0.004 | 0.850 | |
import_scExp | 7.460 | 0.068 | 7.535 | |
inter_correlation_scExp | 0.345 | 0.004 | 0.348 | |
intra_correlation_scExp | 0.364 | 0.004 | 0.368 | |
launchApp | 0.000 | 0.000 | 0.001 | |
normalize_scExp | 0.538 | 0.016 | 0.555 | |
num_cell_after_QC_filt_scExp | 0.617 | 0.004 | 0.620 | |
num_cell_after_cor_filt_scExp | 12.323 | 0.156 | 12.467 | |
num_cell_before_cor_filt_scExp | 0.201 | 0.004 | 0.205 | |
num_cell_in_cluster_scExp | 0.443 | 0.004 | 0.442 | |
num_cell_scExp | 0.473 | 0.000 | 0.473 | |
plot_cluster_consensus_scExp | 0.869 | 0.040 | 0.908 | |
plot_correlation_PCA_scExp | 0.998 | 0.000 | 0.997 | |
plot_coverage_BigWig | 0.206 | 0.000 | 0.205 | |
plot_differential_summary_scExp | 0.223 | 0.000 | 0.223 | |
plot_differential_volcano_scExp | 0.32 | 0.00 | 0.32 | |
plot_distribution_scExp | 0.396 | 0.004 | 0.399 | |
plot_gain_or_loss_barplots | 44.836 | 0.184 | 45.020 | |
plot_heatmap_scExp | 0.302 | 0.000 | 0.302 | |
plot_inter_correlation_scExp | 0.499 | 0.000 | 0.499 | |
plot_intra_correlation_scExp | 0.465 | 0.008 | 0.473 | |
plot_most_contributing_features | 0.390 | 0.008 | 0.398 | |
plot_percent_active_feature_scExp | 1.803 | 0.012 | 1.816 | |
plot_pie_most_contributing_chr | 0.279 | 0.000 | 0.279 | |
plot_reduced_dim_scExp | 2.624 | 0.000 | 2.625 | |
plot_reduced_dim_scExp_CNA | 21.956 | 0.136 | 22.092 | |
plot_top_TF_scExp | 0.439 | 0.000 | 0.439 | |
plot_violin_feature_scExp | 1.799 | 0.028 | 1.827 | |
preprocess_CPM | 0.501 | 0.024 | 0.525 | |
preprocess_RPKM | 0.556 | 0.028 | 0.584 | |
preprocess_TFIDF | 0.495 | 0.016 | 0.511 | |
preprocess_TPM | 0.522 | 0.020 | 0.542 | |
preprocess_feature_size_only | 0.559 | 0.016 | 0.575 | |
preprocessing_filtering_and_reduction | 8.819 | 0.004 | 8.815 | |
read_sparse_matrix | 0 | 0 | 0 | |
rebin_matrix | 7.034 | 0.700 | 21.752 | |
reduce_dims_scExp | 1.681 | 0.100 | 1.781 | |
scExp | 0.998 | 0.052 | 1.050 | |
subsample_scExp | 0.744 | 0.068 | 0.812 | |
subset_bam_call_peaks | 0 | 0 | 0 | |
summary_DA | 0.221 | 0.004 | 0.226 | |
swapAltExp_sameColData | 0.302 | 0.000 | 0.303 | |
table_enriched_genes_scExp | 0.216 | 0.000 | 0.216 | |
wrapper_Signac_FeatureMatrix | 0 | 0 | 0 | |