Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-09 12:07 -0400 (Sat, 09 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" | 4818 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4553 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4595 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4537 |
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 2172/2317 | 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 | |||||||||
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: F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:tidytof.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings tidytof_1.3.0.tar.gz |
StartedAt: 2025-08-09 07:40:05 -0400 (Sat, 09 Aug 2025) |
EndedAt: 2025-08-09 07:48:55 -0400 (Sat, 09 Aug 2025) |
EllapsedTime: 529.3 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: tidytof.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:tidytof.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings tidytof_1.3.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.22-bioc/meat/tidytof.Rcheck' * using R version 4.5.1 (2025-06-13 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: Windows Server 2022 x64 (build 20348) * 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 whether package 'tidytof' can be installed ... OK * used C++ compiler: 'G__~1.EXE (GCC) 14.2.0' * 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 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 for x64 is not available File 'F:/biocbuild/bbs-3.22-bioc/R/library/tidytof/libs/x64/tidytof.dll': Found '_exit', possibly from '_exit' (C) Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf. The detected symbols are linked into the code but might come from libraries and not actually be called. See 'Writing portable packages' in the 'Writing R Extensions' manual. * checking files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed tof_assess_clusters_knn 9.56 0.09 9.69 tof_cluster_flowsom 5.78 0.27 6.15 tof_reduce_umap 4.45 0.08 5.53 * 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 'F:/biocbuild/bbs-3.22-bioc/meat/tidytof.Rcheck/00check.log' for details.
tidytof.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL tidytof ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.22-bioc/R/library' * installing *source* package 'tidytof' ... ** this is package 'tidytof' version '1.3.0' ** using staged installation ** libs using C++ compiler: 'G__~1.EXE (GCC) 14.2.0' g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.22-bioc/R/library/Rcpp/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.22-bioc/R/library/Rcpp/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c code.cpp -o code.o g++ -std=gnu++17 -shared -s -static-libgcc -o tidytof.dll tmp.def RcppExports.o code.o -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.22-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.22-bioc/R/library/00LOCK-tidytof/00new/tidytof/libs/x64 ** 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 ** 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 ucrt) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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 0.14 0.09 0.26
tidytof.Rcheck/tests/testthat.Rout.fail
R version 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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 | 0 | 0 | |
as_flowFrame | 0 | 0 | 0 | |
as_flowSet | 0 | 0 | 0 | |
as_seurat | 0 | 0 | 0 | |
as_tof_tbl | 0.06 | 0.00 | 0.07 | |
make_flowcore_annotated_data_frame | 0 | 0 | 0 | |
reexports | 0 | 0 | 0 | |
rev_asinh | 0 | 0 | 0 | |
tidytof_example_data | 0 | 0 | 0 | |
tof_analyze_abundance | 0 | 0 | 0 | |
tof_analyze_abundance_diffcyt | 0 | 0 | 0 | |
tof_analyze_abundance_glmm | 0 | 0 | 0 | |
tof_analyze_abundance_ttest | 0 | 0 | 0 | |
tof_analyze_expression | 0.00 | 0.02 | 0.02 | |
tof_analyze_expression_diffcyt | 0 | 0 | 0 | |
tof_analyze_expression_lmm | 0 | 0 | 0 | |
tof_analyze_expression_ttest | 0 | 0 | 0 | |
tof_annotate_clusters | 0.46 | 0.00 | 0.47 | |
tof_apply_classifier | 0 | 0 | 0 | |
tof_assess_channels | 0.11 | 0.00 | 0.11 | |
tof_assess_clusters_distance | 0.49 | 0.09 | 0.57 | |
tof_assess_clusters_entropy | 0.72 | 0.00 | 0.72 | |
tof_assess_clusters_knn | 9.56 | 0.09 | 9.69 | |
tof_assess_flow_rate | 0.76 | 0.02 | 0.78 | |
tof_assess_flow_rate_tibble | 0.19 | 0.00 | 0.19 | |
tof_assess_model | 0.49 | 0.02 | 0.53 | |
tof_batch_correct | 0 | 0 | 0 | |
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 | 0 | 0 | |
tof_cluster | 0.64 | 0.00 | 0.65 | |
tof_cluster_ddpr | 0.2 | 0.0 | 0.2 | |
tof_cluster_flowsom | 5.78 | 0.27 | 6.15 | |
tof_cluster_kmeans | 0.03 | 0.00 | 0.03 | |
tof_cluster_phenograph | 2.17 | 0.06 | 2.23 | |
tof_cosine_dist | 0 | 0 | 0 | |
tof_create_grid | 0.07 | 0.02 | 0.08 | |
tof_downsample | 0.23 | 0.00 | 0.23 | |
tof_downsample_constant | 0.11 | 0.00 | 0.11 | |
tof_downsample_density | 0.61 | 0.01 | 0.63 | |
tof_downsample_prop | 0.09 | 0.00 | 0.10 | |
tof_estimate_density | 0.39 | 0.00 | 0.39 | |
tof_extract_central_tendency | 0.2 | 0.0 | 0.2 | |
tof_extract_emd | 0.64 | 0.03 | 0.70 | |
tof_extract_features | 1.07 | 0.00 | 1.07 | |
tof_extract_jsd | 0.72 | 0.02 | 0.74 | |
tof_extract_proportion | 0.14 | 0.01 | 0.15 | |
tof_extract_threshold | 0.24 | 0.00 | 0.24 | |
tof_find_knn | 0.25 | 0.10 | 0.34 | |
tof_generate_palette | 0 | 0 | 0 | |
tof_get_model_mixture | 0.31 | 0.01 | 0.33 | |
tof_get_model_outcomes | 0.25 | 0.00 | 0.25 | |
tof_get_model_penalty | 0.28 | 0.02 | 0.30 | |
tof_get_model_training_data | 0.36 | 0.01 | 0.37 | |
tof_get_model_type | 0.22 | 0.00 | 0.22 | |
tof_get_model_x | 0.22 | 0.00 | 0.22 | |
tof_get_model_y | 0.31 | 0.00 | 0.32 | |
tof_get_panel | 0.05 | 0.00 | 0.04 | |
tof_log_rank_test | 0 | 0 | 0 | |
tof_make_knn_graph | 0 | 0 | 0 | |
tof_make_roc_curve | 0.39 | 0.00 | 0.39 | |
tof_metacluster | 0.88 | 0.08 | 0.96 | |
tof_metacluster_consensus | 0.33 | 0.03 | 0.36 | |
tof_metacluster_flowsom | 0.82 | 0.03 | 0.86 | |
tof_metacluster_hierarchical | 0.08 | 0.00 | 0.07 | |
tof_metacluster_kmeans | 0.08 | 0.00 | 0.08 | |
tof_metacluster_phenograph | 0.11 | 0.00 | 0.11 | |
tof_plot_cells_density | 0.05 | 0.00 | 0.05 | |
tof_plot_cells_embedding | 3.70 | 0.05 | 4.05 | |
tof_plot_cells_layout | 3.24 | 0.02 | 3.27 | |
tof_plot_cells_scatter | 0 | 0 | 0 | |
tof_plot_clusters_heatmap | 0.09 | 0.00 | 0.11 | |
tof_plot_clusters_mst | 0.33 | 0.01 | 0.34 | |
tof_plot_clusters_volcano | 0.05 | 0.00 | 0.05 | |
tof_plot_model | 0.84 | 0.00 | 0.84 | |
tof_plot_sample_features | 0.14 | 0.00 | 0.14 | |
tof_plot_sample_heatmap | 0.08 | 0.00 | 0.08 | |
tof_postprocess | 0.09 | 0.00 | 0.09 | |
tof_predict | 0.35 | 0.00 | 0.35 | |
tof_preprocess | 0.22 | 0.02 | 0.23 | |
tof_read_data | 0.12 | 0.00 | 0.13 | |
tof_reduce_dimensions | 2.91 | 0.08 | 3.01 | |
tof_reduce_pca | 0.2 | 0.0 | 0.2 | |
tof_reduce_tsne | 1.08 | 0.01 | 1.10 | |
tof_reduce_umap | 4.45 | 0.08 | 5.53 | |
tof_set_panel | 0.06 | 0.02 | 0.08 | |
tof_spade_density | 0.55 | 0.00 | 0.54 | |
tof_split_data | 0.06 | 0.00 | 0.07 | |
tof_split_tidytof_reduced_dimensions | 0 | 0 | 0 | |
tof_train_model | 1.64 | 0.00 | 1.64 | |
tof_transform | 0.16 | 0.01 | 0.17 | |
tof_upsample | 0.31 | 0.00 | 0.31 | |
tof_upsample_distance | 0.52 | 0.00 | 0.52 | |
tof_upsample_neighbor | 0.08 | 0.00 | 0.08 | |
tof_write_data | 0 | 0 | 0 | |
tof_write_fcs | 0 | 0 | 0 | |
where | 0 | 0 | 0 | |