Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:31 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the ChromSCape package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 306/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ChromSCape 1.2.62 (landing page) Pacome Prompsy
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: ChromSCape |
Version: 1.2.62 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ChromSCape.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ChromSCape_1.2.62.tar.gz |
StartedAt: 2021-10-14 17:23:35 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 17:39:53 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 977.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ChromSCape.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ChromSCape.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ChromSCape_1.2.62.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/ChromSCape.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ChromSCape/DESCRIPTION’ ... OK * this is package ‘ChromSCape’ version ‘1.2.62’ * 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 * 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 dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE CompareWilcox: no visible binding for global variable ‘annot.’ bams_to_matrix_indexes: no visible binding for global variable ‘files_dir_list’ filter_correlated_cell_scExp: no visible binding for global variable ‘run_tsne’ 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_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_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’ subset_bam_call_peaks: no visible binding for global variable ‘merged_bam’ Undefined global functions or variables: Fri_cyto Gain_or_Loss V1 V2 absolute_value annot. cluster clusterConsensus cytoBand files_dir_list genes k merged_bam ncells run_tsne sample_id total_counts * 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 ... OK * checking Rd \usage sections ... OK * 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 91.493 0.394 91.982 plot_reduced_dim_scExp_CNA 44.824 0.138 44.997 calculate_CNA 41.568 2.555 44.206 get_most_variable_cyto 42.717 0.138 42.884 calculate_cyto_mat 40.518 1.126 41.692 calculate_gain_or_loss 38.337 0.815 39.188 calculate_logRatio_CNA 36.559 1.163 37.813 get_cyto_features 37.347 0.091 37.462 peaks_to_bins 14.600 8.534 8.077 num_cell_after_cor_filt_scExp 10.684 0.093 10.786 filter_correlated_cell_scExp 10.001 0.182 10.189 CompareedgeRGLM 8.815 0.490 9.309 differential_analysis_scExp 6.661 2.359 4.723 CompareWilcox 7.038 1.145 5.927 create_scDataset_raw 7.553 0.560 8.120 import_scExp 6.750 0.065 6.824 choose_cluster_scExp 5.354 0.815 6.185 reduce_dims_scExp 5.886 0.233 6.123 consensus_clustering_scExp 4.648 0.964 5.622 * 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 ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 4 NOTEs See ‘/Users/biocbuild/bbs-3.13-bioc/meat/ChromSCape.Rcheck/00check.log’ for details.
ChromSCape.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ChromSCape ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘ChromSCape’ ... ** using staged installation ** libs clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c as_dist.cpp -o as_dist.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/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/4.1/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 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (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 0 | SKIP 0 | PASS 11 ] > > proc.time() user system elapsed 46.189 3.822 49.836
ChromSCape.Rcheck/ChromSCape-Ex.timings
name | user | system | elapsed | |
CompareWilcox | 7.038 | 1.145 | 5.927 | |
CompareedgeRGLM | 8.815 | 0.490 | 9.309 | |
annotToCol2 | 2.091 | 0.061 | 2.151 | |
calculate_CNA | 41.568 | 2.555 | 44.206 | |
calculate_cyto_mat | 40.518 | 1.126 | 41.692 | |
calculate_gain_or_loss | 38.337 | 0.815 | 39.188 | |
calculate_logRatio_CNA | 36.559 | 1.163 | 37.813 | |
choose_cluster_scExp | 5.354 | 0.815 | 6.185 | |
colors_scExp | 0.390 | 0.003 | 0.392 | |
consensus_clustering_scExp | 4.648 | 0.964 | 5.622 | |
correlation_and_hierarchical_clust_scExp | 0.382 | 0.002 | 0.383 | |
create_project_folder | 0.001 | 0.002 | 0.003 | |
create_scDataset_raw | 7.553 | 0.560 | 8.120 | |
create_scExp | 1.683 | 0.027 | 1.715 | |
define_feature | 0.308 | 0.022 | 0.330 | |
detect_samples | 1.114 | 0.054 | 1.168 | |
differential_analysis_scExp | 6.661 | 2.359 | 4.723 | |
exclude_features_scExp | 2.149 | 0.216 | 2.367 | |
feature_annotation_scExp | 4.176 | 0.250 | 4.428 | |
filter_correlated_cell_scExp | 10.001 | 0.182 | 10.189 | |
filter_scExp | 2.316 | 0.033 | 2.356 | |
find_top_features | 0.434 | 0.010 | 0.444 | |
gene_set_enrichment_analysis_scExp | 0.206 | 0.004 | 0.211 | |
generate_analysis | 0.001 | 0.000 | 0.001 | |
generate_coverage_tracks | 0.000 | 0.000 | 0.001 | |
getExperimentNames | 0.282 | 0.010 | 0.293 | |
getMainExperiment | 0.423 | 0.058 | 0.482 | |
get_cyto_features | 37.347 | 0.091 | 37.462 | |
get_genomic_coordinates | 1.735 | 0.155 | 1.893 | |
get_most_variable_cyto | 42.717 | 0.138 | 42.884 | |
has_genomic_coordinates | 2.677 | 0.151 | 2.832 | |
import_scExp | 6.750 | 0.065 | 6.824 | |
inter_correlation_scExp | 0.888 | 0.012 | 0.900 | |
intra_correlation_scExp | 1.152 | 0.014 | 1.167 | |
launchApp | 0.000 | 0.001 | 0.000 | |
normalize_scExp | 1.784 | 0.104 | 1.888 | |
num_cell_after_QC_filt_scExp | 1.947 | 0.016 | 1.963 | |
num_cell_after_cor_filt_scExp | 10.684 | 0.093 | 10.786 | |
num_cell_before_cor_filt_scExp | 0.219 | 0.003 | 0.222 | |
num_cell_in_cluster_scExp | 0.926 | 0.005 | 0.932 | |
num_cell_scExp | 1.633 | 0.013 | 1.647 | |
peaks_to_bins | 14.600 | 8.534 | 8.077 | |
plot_cluster_consensus_scExp | 1.172 | 0.025 | 1.198 | |
plot_coverage_BigWig | 1.005 | 0.018 | 1.023 | |
plot_differential_H1_scExp | 0.201 | 0.004 | 0.205 | |
plot_differential_summary_scExp | 0.234 | 0.005 | 0.238 | |
plot_differential_volcano_scExp | 0.276 | 0.013 | 0.289 | |
plot_distribution_scExp | 0.717 | 0.017 | 0.736 | |
plot_gain_or_loss_barplots | 91.493 | 0.394 | 91.982 | |
plot_heatmap_scExp | 0.441 | 0.011 | 0.452 | |
plot_inter_correlation_scExp | 0.943 | 0.006 | 0.950 | |
plot_intra_correlation_scExp | 0.945 | 0.007 | 0.952 | |
plot_most_contributing_features | 0.585 | 0.007 | 0.593 | |
plot_pie_most_contributing_chr | 0.406 | 0.007 | 0.412 | |
plot_reduced_dim_scExp | 3.768 | 0.034 | 3.809 | |
plot_reduced_dim_scExp_CNA | 44.824 | 0.138 | 44.997 | |
preprocess_CPM | 1.761 | 0.142 | 1.903 | |
preprocess_RPKM | 1.917 | 0.060 | 1.978 | |
preprocess_TFIDF | 1.976 | 0.143 | 2.120 | |
preprocess_TPM | 1.786 | 0.113 | 1.900 | |
preprocess_feature_size_only | 1.756 | 0.056 | 1.813 | |
read_sparse_matrix | 0.000 | 0.001 | 0.001 | |
reduce_dims_scExp | 5.886 | 0.233 | 6.123 | |
scExp | 1.689 | 0.020 | 1.715 | |
subsample_scExp | 2.273 | 0.027 | 2.302 | |
subset_bam_call_peaks | 0 | 0 | 0 | |
swapAltExp_sameColData | 0.503 | 0.004 | 0.507 | |
table_enriched_genes_scExp | 0.216 | 0.003 | 0.218 | |
wrapper_Signac_FeatureMatrix | 0.000 | 0.000 | 0.001 | |