##############################################################################
##############################################################################
###
### 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_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/tidytof.Rcheck’
* using R version 4.6.0 Patched (2026-04-24 r89963)
* using platform: aarch64-apple-darwin23
* R was compiled by
    Apple clang version 17.0.0 (clang-1700.3.19.1)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-04-30 02:37:15 UTC
* using option ‘--no-vignettes’
* checking for file ‘tidytof/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘tidytof’ version ‘1.6.0’
* 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 17.0.0 (clang-1700.6.4.2)’
* used SDK: ‘MacOSX26.2.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 whether startup messages can be suppressed ... 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 ... INFO
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘tidytof-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: tof_metacluster_flowsom
> ### Title: Metacluster clustered CyTOF data using FlowSOM's built-in
> ###   metaclustering algorithm
> ### Aliases: tof_metacluster_flowsom
> 
> ### ** Examples
> 
> sim_data <-
+     dplyr::tibble(
+         cd45 = rnorm(n = 1000),
+         cd38 = rnorm(n = 1000),
+         cd34 = rnorm(n = 1000),
+         cd19 = rnorm(n = 1000),
+         cluster_id = sample(letters, size = 1000, replace = TRUE)
+     )
> 
> tof_metacluster_flowsom(
+     tof_tibble = sim_data,
+     cluster_col = cluster_id,
+     clustering_algorithm = "consensus"
+ )
# A tibble: 1,000 × 1
   .flowsom_metacluster
   <chr>               
 1 4                   
 2 1                   
 3 4                   
 4 4                   
 5 4                   
 6 1                   
 7 4                   
 8 4                   
 9 4                   
10 4                   
# ℹ 990 more rows
> 
> tof_metacluster_flowsom(
+     tof_tibble = sim_data,
+     cluster_col = cluster_id,
+     clustering_algorithm = "som"
+ )
Error in minimum_spanning_tree_prim_impl(graph = graph, weights = weights) : 
  REAL() can only be applied to a 'numeric', not a 'NULL'
Calls: tof_metacluster_flowsom ... <Anonymous> -> mst -> minimum_spanning_tree_prim_impl
Execution halted
* 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:
   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 3 | WARN 20 | SKIP 1 | PASS 676 ]
  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: 2 ERRORs
See
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/tidytof.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL tidytof
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’
* installing *source* package ‘tidytof’ ...
** this is package ‘tidytof’ version ‘1.6.0’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
using SDK: ‘MacOSX26.2.sdk’
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/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++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/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++20 -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/4.6/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
Warning in fun(libname, pkgname) :
  Package 'tidytof' is deprecated and will be removed from Bioconductor
  version 3.24
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'tidytof' is deprecated and will be removed from Bioconductor
  version 3.24
** testing if installed package keeps a record of temporary installation path
* DONE (tidytof)

R version 4.6.0 Patched (2026-04-24 r89963) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23

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 
  0.079   0.026   0.099 

R version 4.6.0 Patched (2026-04-24 r89963) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23

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)
Warning message:
In fun(libname, pkgname) :
  Package 'tidytof' is deprecated and will be removed from Bioconductor
  version 3.24
> test_check("tidytof")

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Loading required namespace: diffcyt

Attaching package: 'readr'

The following objects are masked from 'package:testthat':

    edition_get, local_edition

Saving _problems/test-metaclustering-197.R
Saving _problems/test-patient-level_modeling-1052.R
Saving _problems/test-visualization-555.R
[ FAIL 3 | WARN 20 | SKIP 1 | PASS 676 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1):

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-metaclustering.R:192:5'): metaclustering result is the right shape ──
Error in `minimum_spanning_tree_prim_impl(graph = graph, weights = weights)`: REAL() can only be applied to a 'numeric', not a 'NULL'
Backtrace:
     ▆
  1. └─tidytof::tof_metacluster_flowsom(...) at test-metaclustering.R:192:5
  2.   └─tidytof:::MetaClustering(...)
  3.     └─tidytof:::DetermineNumberOfClusters(...)
  4.       └─tidytof (local) method(data, k = i, ...)
  5.         ├─base::suppressMessages(...)
  6.         │ └─base::withCallingHandlers(...)
  7.         └─FlowSOM::SOM(data, xdim = k, ydim = 1, rlen = 100)
  8.           └─FlowSOM:::Dist.MST(codes)
  9.             └─igraph::minimum.spanning.tree(fullGraph)
 10.               └─igraph::mst(...)
 11.                 └─igraph:::minimum_spanning_tree_prim_impl(graph = graph, weights = weights)
── 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 3 | WARN 20 | SKIP 1 | PASS 676 ]
Error:
! Test failures.
Execution halted