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This page was generated on 2025-09-18 11:40 -0400 (Thu, 18 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4827
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4608
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4549
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4581
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 2193/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
tidytof 1.2.0  (landing page)
Timothy Keyes
Snapshot Date: 2025-09-15 13:40 -0400 (Mon, 15 Sep 2025)
git_url: https://git.bioconductor.org/packages/tidytof
git_branch: RELEASE_3_21
git_last_commit: d95118e
git_last_commit_date: 2025-04-15 13:39:34 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    ERROR  
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    ERROR    OK  
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    TIMEOUT  skipped


CHECK results for tidytof on kjohnson1

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.

raw results


Summary

Package: tidytof
Version: 1.2.0
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_1.2.0.tar.gz
StartedAt: 2025-09-17 14:10:16 -0400 (Wed, 17 Sep 2025)
EndedAt: 2025-09-17 14:18:24 -0400 (Wed, 17 Sep 2025)
EllapsedTime: 488.3 seconds
RetCode: 1
Status:   ERROR  
CheckDir: tidytof.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### 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_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/tidytof.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘tidytof/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘tidytof’ version ‘1.2.0’
* 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 15.0.0 (clang-1500.0.40.1)’
* 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  8.109  0.102   8.611
tof_cluster_flowsom      5.133  0.871   6.420
tof_plot_cells_layout    5.023  0.041   5.302
tof_reduce_umap          4.924  0.045   5.057
tof_plot_cells_embedding 4.054  0.308   5.062
* 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-3.21-bioc/meat/tidytof.Rcheck/00check.log’
for details.


Installation output

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-arm64/Resources/library’
* installing *source* package ‘tidytof’ ...
** this is package ‘tidytof’ version ‘1.2.0’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c code.cpp -o code.o
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o tidytof.so RcppExports.o code.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.5-arm64/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)

Tests output

tidytof.Rcheck/tests/spelling.Rout


R version 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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
+     )
+ }
All Done!
> 
> proc.time()
   user  system elapsed 
  0.210   0.070   0.272 

tidytof.Rcheck/tests/testthat.Rout.fail


R version 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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

Example timings

tidytof.Rcheck/tidytof-Ex.timings

nameusersystemelapsed
as_SingleCellExperiment0.0000.0010.000
as_flowFrame0.0000.0000.001
as_flowSet0.0000.0000.001
as_seurat0.0000.0000.001
as_tof_tbl0.4840.0060.501
make_flowcore_annotated_data_frame000
reexports000
rev_asinh0.0000.0000.001
tidytof_example_data0.0020.0010.003
tof_analyze_abundance000
tof_analyze_abundance_diffcyt000
tof_analyze_abundance_glmm000
tof_analyze_abundance_ttest0.0000.0010.000
tof_analyze_expression0.0000.0000.001
tof_analyze_expression_diffcyt000
tof_analyze_expression_lmm000
tof_analyze_expression_ttest000
tof_annotate_clusters0.1050.0060.114
tof_apply_classifier000
tof_assess_channels0.0820.0020.085
tof_assess_clusters_distance0.4570.0450.529
tof_assess_clusters_entropy0.6890.0490.757
tof_assess_clusters_knn8.1090.1028.611
tof_assess_flow_rate1.0350.0371.135
tof_assess_flow_rate_tibble0.2510.0070.265
tof_assess_model0.3680.0100.388
tof_batch_correct000
tof_batch_correct_quantile000
tof_batch_correct_quantile_tibble0.0010.0000.000
tof_batch_correct_rescale000
tof_calculate_flow_rate0.0170.0000.017
tof_cluster0.4360.0160.470
tof_cluster_ddpr0.1690.0040.180
tof_cluster_flowsom5.1330.8716.420
tof_cluster_kmeans0.0360.0010.039
tof_cluster_phenograph1.5190.0321.595
tof_cosine_dist000
tof_create_grid0.0490.0010.049
tof_downsample0.1690.0030.180
tof_downsample_constant0.0630.0010.065
tof_downsample_density0.7320.0090.757
tof_downsample_prop0.0990.0050.107
tof_estimate_density0.5220.0070.540
tof_extract_central_tendency0.1580.0020.163
tof_extract_emd0.4220.0080.446
tof_extract_features0.5120.0050.529
tof_extract_jsd0.5050.0490.583
tof_extract_proportion0.1340.0010.143
tof_extract_threshold0.1620.0020.170
tof_find_knn0.2750.1940.487
tof_generate_palette000
tof_get_model_mixture0.2670.0030.279
tof_get_model_outcomes0.2380.0020.249
tof_get_model_penalty0.2370.0020.245
tof_get_model_training_data0.2700.0020.276
tof_get_model_type0.2410.0010.245
tof_get_model_x0.2290.0030.232
tof_get_model_y0.2710.0020.274
tof_get_panel0.0390.0020.042
tof_log_rank_test000
tof_make_knn_graph000
tof_make_roc_curve0.3220.0030.333
tof_metacluster1.0530.0601.207
tof_metacluster_consensus0.1540.0170.184
tof_metacluster_flowsom0.4260.0290.482
tof_metacluster_hierarchical0.0320.0010.064
tof_metacluster_kmeans0.0360.0010.058
tof_metacluster_phenograph0.0610.0030.067
tof_plot_cells_density0.0780.0020.083
tof_plot_cells_embedding4.0540.3085.062
tof_plot_cells_layout5.0230.0415.302
tof_plot_cells_scatter0.0030.0010.005
tof_plot_clusters_heatmap0.1210.0060.131
tof_plot_clusters_mst0.2590.0130.304
tof_plot_clusters_volcano0.0800.0010.082
tof_plot_model0.6890.0070.742
tof_plot_sample_features0.1700.0020.175
tof_plot_sample_heatmap0.1070.0020.112
tof_postprocess0.0970.0030.102
tof_predict0.2640.0030.274
tof_preprocess0.1620.0040.169
tof_read_data0.0770.0020.081
tof_reduce_dimensions2.2250.0372.329
tof_reduce_pca0.1630.0020.172
tof_reduce_tsne1.2100.0281.318
tof_reduce_umap4.9240.0455.057
tof_set_panel0.0850.0020.089
tof_spade_density0.7440.0100.768
tof_split_data0.0570.0020.059
tof_split_tidytof_reduced_dimensions000
tof_train_model1.4250.0231.503
tof_transform0.1600.0030.165
tof_upsample0.2320.0030.239
tof_upsample_distance0.3060.0050.316
tof_upsample_neighbor0.0740.0030.077
tof_write_data000
tof_write_fcs000
where000