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This page was generated on 2025-08-01 12:09 -0400 (Fri, 01 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4796
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4534
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4578
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4519
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (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 2168/2313HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
tidytof 1.3.0  (landing page)
Timothy Keyes
Snapshot Date: 2025-07-31 13:25 -0400 (Thu, 31 Jul 2025)
git_url: https://git.bioconductor.org/packages/tidytof
git_branch: devel
git_last_commit: 7757e98
git_last_commit_date: 2025-04-15 13:39:34 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    ERROR  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    ERROR    OK  
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    ERROR  


CHECK results for tidytof on lconway

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: 1.3.0
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

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_1.3.0.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.


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-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)

Tests output

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

Example timings

tidytof.Rcheck/tidytof-Ex.timings

nameusersystemelapsed
as_SingleCellExperiment0.0000.0000.001
as_flowFrame000
as_flowSet000
as_seurat0.0000.0010.000
as_tof_tbl0.0550.0030.060
make_flowcore_annotated_data_frame0.0000.0000.001
reexports000
rev_asinh0.0000.0010.001
tidytof_example_data0.0030.0010.004
tof_analyze_abundance000
tof_analyze_abundance_diffcyt0.0010.0000.001
tof_analyze_abundance_glmm0.0000.0010.000
tof_analyze_abundance_ttest000
tof_analyze_expression0.0000.0010.000
tof_analyze_expression_diffcyt000
tof_analyze_expression_lmm000
tof_analyze_expression_ttest000
tof_annotate_clusters0.4360.0070.444
tof_apply_classifier0.0000.0010.000
tof_assess_channels0.0900.0010.091
tof_assess_clusters_distance0.4480.0370.489
tof_assess_clusters_entropy0.6990.0220.724
tof_assess_clusters_knn9.2490.0799.376
tof_assess_flow_rate0.7660.0110.782
tof_assess_flow_rate_tibble0.1870.0020.192
tof_assess_model0.4790.0090.493
tof_batch_correct0.0000.0000.001
tof_batch_correct_quantile000
tof_batch_correct_quantile_tibble000
tof_batch_correct_rescale000
tof_calculate_flow_rate0.0130.0010.013
tof_cluster0.5380.0140.553
tof_cluster_ddpr0.1930.0020.196
tof_cluster_flowsom4.9370.9045.916
tof_cluster_kmeans0.0300.0000.031
tof_cluster_phenograph1.6810.0411.728
tof_cosine_dist000
tof_create_grid0.0470.0010.047
tof_downsample0.1690.0020.171
tof_downsample_constant0.0690.0010.071
tof_downsample_density0.5690.0040.575
tof_downsample_prop0.0760.0010.076
tof_estimate_density0.3940.0100.407
tof_extract_central_tendency0.1720.0020.176
tof_extract_emd0.8630.0440.914
tof_extract_features0.6050.0100.620
tof_extract_jsd0.6220.0620.711
tof_extract_proportion0.1410.0020.144
tof_extract_threshold0.1760.0020.178
tof_find_knn0.2190.2190.440
tof_generate_palette000
tof_get_model_mixture0.2700.0030.274
tof_get_model_outcomes0.2320.0020.236
tof_get_model_penalty0.2400.0020.243
tof_get_model_training_data0.2780.0020.281
tof_get_model_type0.2270.0010.229
tof_get_model_x0.2530.0020.256
tof_get_model_y0.2400.0020.243
tof_get_panel0.0350.0010.037
tof_log_rank_test000
tof_make_knn_graph000
tof_make_roc_curve0.3220.0030.325
tof_metacluster0.7570.0490.820
tof_metacluster_consensus0.3000.0220.326
tof_metacluster_flowsom0.7590.0440.814
tof_metacluster_hierarchical0.0640.0000.065
tof_metacluster_kmeans0.0600.0000.061
tof_metacluster_phenograph0.0780.0010.080
tof_plot_cells_density0.0390.0010.039
tof_plot_cells_embedding2.9930.1193.163
tof_plot_cells_layout3.0450.0153.073
tof_plot_cells_scatter0.0030.0010.003
tof_plot_clusters_heatmap0.0690.0010.070
tof_plot_clusters_mst0.2430.0090.253
tof_plot_clusters_volcano0.0370.0000.038
tof_plot_model0.6510.0040.658
tof_plot_sample_features0.1020.0010.104
tof_plot_sample_heatmap0.0510.0010.052
tof_postprocess0.1010.0020.103
tof_predict0.2720.0030.276
tof_preprocess0.1530.0020.156
tof_read_data0.0760.0020.078
tof_reduce_dimensions2.3200.0412.362
tof_reduce_pca0.1640.0020.168
tof_reduce_tsne0.8150.0300.853
tof_reduce_umap3.4230.0583.450
tof_set_panel0.0870.0020.089
tof_spade_density0.5210.0070.531
tof_split_data0.0550.0010.057
tof_split_tidytof_reduced_dimensions0.0000.0000.001
tof_train_model1.6490.0171.673
tof_transform0.1710.0030.174
tof_upsample0.2510.0030.256
tof_upsample_distance0.3770.0040.384
tof_upsample_neighbor0.0600.0010.061
tof_write_data0.0000.0010.000
tof_write_fcs0.0000.0010.000
where000