Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-01 12:09 -0400 (Fri, 01 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4796 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4534 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4578 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4519 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4517 |
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 2168/2313 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
tidytof 1.3.0 (landing page) Timothy Keyes
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | ERROR | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
To the developers/maintainers of the tidytof package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/tidytof.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: tidytof |
Version: 1.3.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:tidytof.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings tidytof_1.3.0.tar.gz |
StartedAt: 2025-08-01 00:35:46 -0400 (Fri, 01 Aug 2025) |
EndedAt: 2025-08-01 00:42:49 -0400 (Fri, 01 Aug 2025) |
EllapsedTime: 422.8 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: tidytof.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:tidytof.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings tidytof_1.3.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/tidytof.Rcheck’ * using R version 4.5.1 (2025-06-13) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘tidytof/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘tidytof’ version ‘1.3.0’ * 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 ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘tidytof’ 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 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 ... OK * checking Rd files ... OK * 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 R/sysdata.rda ... 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 tof_assess_clusters_knn 9.249 0.079 9.376 tof_cluster_flowsom 4.937 0.904 5.916 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘spelling.R’ Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: 9. └─yardstick::curve_metric_summarizer(...) 10. └─yardstick:::yardstick_eval_select_dots(..., data = data, error_call = error_call) 11. └─tidyselect::eval_select(...) 12. └─tidyselect:::eval_select_impl(...) 13. ├─tidyselect:::with_subscript_errors(...) 14. │ └─base::withCallingHandlers(...) 15. └─tidyselect:::vars_select_eval(...) 16. └─tidyselect:::ensure_named(...) 17. └─tidyselect:::check_empty(pos, allow_empty, call = call) 18. └─cli::cli_abort("Must select at least one item.", call = call) 19. └─rlang::abort(...) [ FAIL 2 | WARN 1 | SKIP 0 | PASS 684 ] Error: Test failures Execution halted * 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: 1 ERROR, 1 NOTE See ‘/Users/biocbuild/bbs-3.22-bioc/meat/tidytof.Rcheck/00check.log’ for details.
tidytof.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL tidytof ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘tidytof’ ... ** this is package ‘tidytof’ version ‘1.3.0’ ** 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/4.5-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/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c code.cpp -o code.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 tidytof.so RcppExports.o code.o -F/Library/Frameworks/R.framework/.. -framework R installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-tidytof/00new/tidytof/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (tidytof)
tidytof.Rcheck/tests/spelling.Rout
R version 4.5.1 (2025-06-13) -- "Great Square Root" Copyright (C) 2025 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. > if (requireNamespace("spelling", quietly = TRUE)) { + spelling::spell_check_test( + vignettes = TRUE, error = FALSE, + skip_on_cran = TRUE + ) + } NULL > > proc.time() user system elapsed 0.192 0.077 0.264
tidytof.Rcheck/tests/testthat.Rout.fail
R version 4.5.1 (2025-06-13) -- "Great Square Root" Copyright (C) 2025 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. > Sys.setenv(R_TESTS="") > library(testthat) > library(tidytof) Attaching package: 'tidytof' The following object is masked from 'package:testthat': matches > test_check("tidytof") Attaching package: 'dplyr' The following object is masked from 'package:testthat': matches The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union Attaching package: 'purrr' The following object is masked from 'package:testthat': is_null Attaching package: 'tidyr' The following object is masked from 'package:testthat': matches Loading required namespace: diffcyt Attaching package: 'readr' The following objects are masked from 'package:testthat': edition_get, local_edition [ FAIL 2 | WARN 1 | SKIP 0 | PASS 684 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-patient-level_modeling.R:1050:1'): (code run outside of `test_that()`) ── Error in `yardstick::roc_curve(dplyr::mutate(input_data, truth = dplyr::pull(input_data, { { truth_col } })), { { prob_cols } }, truth = "truth", event_level = "second")`: Must select at least one item. Backtrace: ▆ 1. └─tidytof::tof_assess_model(bootstrap_multinomial_regression, new_data = feature_tibble) at test-patient-level_modeling.R:1050:1 2. └─tidytof:::tof_assess_model_new_data(tof_model = tof_model, new_data = new_data) 3. └─tidytof::tof_make_roc_curve(...) 4. ├─dplyr::mutate(...) 5. ├─yardstick::roc_curve(...) 6. └─yardstick:::roc_curve.data.frame(...) 7. └─yardstick::curve_metric_summarizer(...) 8. └─yardstick:::yardstick_eval_select_dots(..., data = data, error_call = error_call) 9. └─tidyselect::eval_select(...) 10. └─tidyselect:::eval_select_impl(...) 11. ├─tidyselect:::with_subscript_errors(...) 12. │ └─base::withCallingHandlers(...) 13. └─tidyselect:::vars_select_eval(...) 14. └─tidyselect:::ensure_named(...) 15. └─tidyselect:::check_empty(pos, allow_empty, call = call) 16. └─cli::cli_abort("Must select at least one item.", call = call) 17. └─rlang::abort(...) ── Error ('test-visualization.R:553:1'): (code run outside of `test_that()`) ─── Error in `yardstick::roc_curve(dplyr::mutate(input_data, truth = dplyr::pull(input_data, { { truth_col } })), { { prob_cols } }, truth = "truth", event_level = "second")`: Must select at least one item. Backtrace: ▆ 1. └─tidytof::tof_plot_model(multinomial_tof_model) at test-visualization.R:553:1 2. └─tidytof:::tof_plot_model_multinomial(...) 3. └─tidytof::tof_assess_model(tof_model = tof_model, new_data = new_data) 4. └─tidytof:::tof_assess_model_new_data(tof_model = tof_model, new_data = new_data) 5. └─tidytof::tof_make_roc_curve(...) 6. ├─dplyr::mutate(...) 7. ├─yardstick::roc_curve(...) 8. └─yardstick:::roc_curve.data.frame(...) 9. └─yardstick::curve_metric_summarizer(...) 10. └─yardstick:::yardstick_eval_select_dots(..., data = data, error_call = error_call) 11. └─tidyselect::eval_select(...) 12. └─tidyselect:::eval_select_impl(...) 13. ├─tidyselect:::with_subscript_errors(...) 14. │ └─base::withCallingHandlers(...) 15. └─tidyselect:::vars_select_eval(...) 16. └─tidyselect:::ensure_named(...) 17. └─tidyselect:::check_empty(pos, allow_empty, call = call) 18. └─cli::cli_abort("Must select at least one item.", call = call) 19. └─rlang::abort(...) [ FAIL 2 | WARN 1 | SKIP 0 | PASS 684 ] Error: Test failures Execution halted
tidytof.Rcheck/tidytof-Ex.timings
name | user | system | elapsed | |
as_SingleCellExperiment | 0.000 | 0.000 | 0.001 | |
as_flowFrame | 0 | 0 | 0 | |
as_flowSet | 0 | 0 | 0 | |
as_seurat | 0.000 | 0.001 | 0.000 | |
as_tof_tbl | 0.055 | 0.003 | 0.060 | |
make_flowcore_annotated_data_frame | 0.000 | 0.000 | 0.001 | |
reexports | 0 | 0 | 0 | |
rev_asinh | 0.000 | 0.001 | 0.001 | |
tidytof_example_data | 0.003 | 0.001 | 0.004 | |
tof_analyze_abundance | 0 | 0 | 0 | |
tof_analyze_abundance_diffcyt | 0.001 | 0.000 | 0.001 | |
tof_analyze_abundance_glmm | 0.000 | 0.001 | 0.000 | |
tof_analyze_abundance_ttest | 0 | 0 | 0 | |
tof_analyze_expression | 0.000 | 0.001 | 0.000 | |
tof_analyze_expression_diffcyt | 0 | 0 | 0 | |
tof_analyze_expression_lmm | 0 | 0 | 0 | |
tof_analyze_expression_ttest | 0 | 0 | 0 | |
tof_annotate_clusters | 0.436 | 0.007 | 0.444 | |
tof_apply_classifier | 0.000 | 0.001 | 0.000 | |
tof_assess_channels | 0.090 | 0.001 | 0.091 | |
tof_assess_clusters_distance | 0.448 | 0.037 | 0.489 | |
tof_assess_clusters_entropy | 0.699 | 0.022 | 0.724 | |
tof_assess_clusters_knn | 9.249 | 0.079 | 9.376 | |
tof_assess_flow_rate | 0.766 | 0.011 | 0.782 | |
tof_assess_flow_rate_tibble | 0.187 | 0.002 | 0.192 | |
tof_assess_model | 0.479 | 0.009 | 0.493 | |
tof_batch_correct | 0.000 | 0.000 | 0.001 | |
tof_batch_correct_quantile | 0 | 0 | 0 | |
tof_batch_correct_quantile_tibble | 0 | 0 | 0 | |
tof_batch_correct_rescale | 0 | 0 | 0 | |
tof_calculate_flow_rate | 0.013 | 0.001 | 0.013 | |
tof_cluster | 0.538 | 0.014 | 0.553 | |
tof_cluster_ddpr | 0.193 | 0.002 | 0.196 | |
tof_cluster_flowsom | 4.937 | 0.904 | 5.916 | |
tof_cluster_kmeans | 0.030 | 0.000 | 0.031 | |
tof_cluster_phenograph | 1.681 | 0.041 | 1.728 | |
tof_cosine_dist | 0 | 0 | 0 | |
tof_create_grid | 0.047 | 0.001 | 0.047 | |
tof_downsample | 0.169 | 0.002 | 0.171 | |
tof_downsample_constant | 0.069 | 0.001 | 0.071 | |
tof_downsample_density | 0.569 | 0.004 | 0.575 | |
tof_downsample_prop | 0.076 | 0.001 | 0.076 | |
tof_estimate_density | 0.394 | 0.010 | 0.407 | |
tof_extract_central_tendency | 0.172 | 0.002 | 0.176 | |
tof_extract_emd | 0.863 | 0.044 | 0.914 | |
tof_extract_features | 0.605 | 0.010 | 0.620 | |
tof_extract_jsd | 0.622 | 0.062 | 0.711 | |
tof_extract_proportion | 0.141 | 0.002 | 0.144 | |
tof_extract_threshold | 0.176 | 0.002 | 0.178 | |
tof_find_knn | 0.219 | 0.219 | 0.440 | |
tof_generate_palette | 0 | 0 | 0 | |
tof_get_model_mixture | 0.270 | 0.003 | 0.274 | |
tof_get_model_outcomes | 0.232 | 0.002 | 0.236 | |
tof_get_model_penalty | 0.240 | 0.002 | 0.243 | |
tof_get_model_training_data | 0.278 | 0.002 | 0.281 | |
tof_get_model_type | 0.227 | 0.001 | 0.229 | |
tof_get_model_x | 0.253 | 0.002 | 0.256 | |
tof_get_model_y | 0.240 | 0.002 | 0.243 | |
tof_get_panel | 0.035 | 0.001 | 0.037 | |
tof_log_rank_test | 0 | 0 | 0 | |
tof_make_knn_graph | 0 | 0 | 0 | |
tof_make_roc_curve | 0.322 | 0.003 | 0.325 | |
tof_metacluster | 0.757 | 0.049 | 0.820 | |
tof_metacluster_consensus | 0.300 | 0.022 | 0.326 | |
tof_metacluster_flowsom | 0.759 | 0.044 | 0.814 | |
tof_metacluster_hierarchical | 0.064 | 0.000 | 0.065 | |
tof_metacluster_kmeans | 0.060 | 0.000 | 0.061 | |
tof_metacluster_phenograph | 0.078 | 0.001 | 0.080 | |
tof_plot_cells_density | 0.039 | 0.001 | 0.039 | |
tof_plot_cells_embedding | 2.993 | 0.119 | 3.163 | |
tof_plot_cells_layout | 3.045 | 0.015 | 3.073 | |
tof_plot_cells_scatter | 0.003 | 0.001 | 0.003 | |
tof_plot_clusters_heatmap | 0.069 | 0.001 | 0.070 | |
tof_plot_clusters_mst | 0.243 | 0.009 | 0.253 | |
tof_plot_clusters_volcano | 0.037 | 0.000 | 0.038 | |
tof_plot_model | 0.651 | 0.004 | 0.658 | |
tof_plot_sample_features | 0.102 | 0.001 | 0.104 | |
tof_plot_sample_heatmap | 0.051 | 0.001 | 0.052 | |
tof_postprocess | 0.101 | 0.002 | 0.103 | |
tof_predict | 0.272 | 0.003 | 0.276 | |
tof_preprocess | 0.153 | 0.002 | 0.156 | |
tof_read_data | 0.076 | 0.002 | 0.078 | |
tof_reduce_dimensions | 2.320 | 0.041 | 2.362 | |
tof_reduce_pca | 0.164 | 0.002 | 0.168 | |
tof_reduce_tsne | 0.815 | 0.030 | 0.853 | |
tof_reduce_umap | 3.423 | 0.058 | 3.450 | |
tof_set_panel | 0.087 | 0.002 | 0.089 | |
tof_spade_density | 0.521 | 0.007 | 0.531 | |
tof_split_data | 0.055 | 0.001 | 0.057 | |
tof_split_tidytof_reduced_dimensions | 0.000 | 0.000 | 0.001 | |
tof_train_model | 1.649 | 0.017 | 1.673 | |
tof_transform | 0.171 | 0.003 | 0.174 | |
tof_upsample | 0.251 | 0.003 | 0.256 | |
tof_upsample_distance | 0.377 | 0.004 | 0.384 | |
tof_upsample_neighbor | 0.060 | 0.001 | 0.061 | |
tof_write_data | 0.000 | 0.001 | 0.000 | |
tof_write_fcs | 0.000 | 0.001 | 0.000 | |
where | 0 | 0 | 0 | |