Multiple platform build/check report for BioC 3.20 - CHECK results for tidytof on kjohnson1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.3 (2025-02-28) -- "Trophy Case"	4764
palomino8	Windows Server 2022 Datacenter	x64	4.4.3 (2025-02-28 ucrt) -- "Trophy Case"	4495
merida1	macOS 12.7.5 Monterey	x86_64	4.4.3 (2025-02-28) -- "Trophy Case"	4522
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.3 (2025-02-28) -- "Trophy Case"	4449
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.4.3 (2025-02-28) -- "Trophy Case"	4426
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*

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: 1.0.0

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_1.0.0.tar.gz

StartedAt: 2025-04-02 11:25:16 -0400 (Wed, 02 Apr 2025)

EndedAt: 2025-04-02 11:33:03 -0400 (Wed, 02 Apr 2025)

EllapsedTime: 467.7 seconds

RetCode: 0

Status: OK

CheckDir: tidytof.Rcheck

Warnings: 0

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_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/tidytof.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘tidytof/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘tidytof’ version ‘1.0.0’
* 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 8.270  0.059   8.393
tof_cluster_flowsom     5.525  0.931   6.595
tof_plot_cells_layout   5.449  0.021   5.534
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘spelling.R’
  Running ‘testthat.R’
 OK
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.20-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/4.4-arm64/Resources/library’
* installing *source* package ‘tidytof’ ...
** 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/4.4-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/4.4-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 -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-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 4.4.3 (2025-02-28) -- "Trophy Case"
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
+     )
+ }
NULL
> 
> proc.time()
   user  system elapsed 
  0.176   0.058   0.234

tidytof.Rcheck/tests/testthat.Rout


R version 4.4.3 (2025-02-28) -- "Trophy Case"
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 0 | WARN 0 | SKIP 0 | PASS 709 ]
> 
> proc.time()
   user  system elapsed 
243.020   7.162 251.633

Example timings

tidytof.Rcheck/tidytof-Ex.timings

name	user	system	elapsed
as_SingleCellExperiment	0	0	0
as_flowFrame	0	0	0
as_flowSet	0.000	0.000	0.001
as_seurat	0.000	0.000	0.001
as_tof_tbl	0.060	0.006	0.066
make_flowcore_annotated_data_frame	0.000	0.000	0.001
reexports	0	0	0
rev_asinh	0.000	0.001	0.000
tidytof_example_data	0.003	0.001	0.004
tof_analyze_abundance	0	0	0
tof_analyze_abundance_diffcyt	0	0	0
tof_analyze_abundance_glmm	0.000	0.000	0.001
tof_analyze_abundance_ttest	0.000	0.000	0.001
tof_analyze_expression	0	0	0
tof_analyze_expression_diffcyt	0.000	0.001	0.000
tof_analyze_expression_lmm	0	0	0
tof_analyze_expression_ttest	0.000	0.000	0.001
tof_annotate_clusters	0.102	0.012	0.114
tof_apply_classifier	0	0	0
tof_assess_channels	0.081	0.007	0.089
tof_assess_clusters_distance	0.459	0.036	0.499
tof_assess_clusters_entropy	0.665	0.018	0.690
tof_assess_clusters_knn	8.270	0.059	8.393
tof_assess_flow_rate	0.710	0.011	0.723
tof_assess_flow_rate_tibble	0.169	0.003	0.172
tof_assess_model	0.369	0.006	0.375
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	0.018	0.000	0.018
tof_cluster	0.450	0.012	0.463
tof_cluster_ddpr	0.173	0.002	0.174
tof_cluster_flowsom	5.525	0.931	6.595
tof_cluster_kmeans	0.032	0.000	0.033
tof_cluster_phenograph	1.533	0.051	1.594
tof_cosine_dist	0	0	0
tof_create_grid	0.047	0.000	0.048
tof_downsample	0.157	0.006	0.171
tof_downsample_constant	0.061	0.001	0.062
tof_downsample_density	0.721	0.009	0.732
tof_downsample_prop	0.066	0.001	0.067
tof_estimate_density	0.534	0.011	0.547
tof_extract_central_tendency	0.159	0.002	0.171
tof_extract_emd	0.762	0.051	0.815
tof_extract_features	0.556	0.016	0.582
tof_extract_jsd	0.898	0.110	1.064
tof_extract_proportion	0.124	0.002	0.129
tof_extract_threshold	0.159	0.001	0.168
tof_find_knn	0.272	0.183	0.459
tof_generate_palette	0.000	0.001	0.001
tof_get_model_mixture	0.231	0.002	0.234
tof_get_model_outcomes	0.230	0.002	0.232
tof_get_model_penalty	0.239	0.002	0.244
tof_get_model_training_data	0.261	0.002	0.294
tof_get_model_type	0.239	0.002	0.242
tof_get_model_x	0.234	0.003	0.245
tof_get_model_y	0.236	0.003	0.244
tof_get_panel	0.044	0.002	0.046
tof_log_rank_test	0.000	0.000	0.001
tof_make_knn_graph	0	0	0
tof_make_roc_curve	0.334	0.005	0.342
tof_metacluster	0.689	0.052	0.759
tof_metacluster_consensus	0.298	0.023	0.337
tof_metacluster_flowsom	0.748	0.055	0.816
tof_metacluster_hierarchical	0.052	0.001	0.053
tof_metacluster_kmeans	0.055	0.001	0.055
tof_metacluster_phenograph	0.073	0.002	0.077
tof_plot_cells_density	0.036	0.001	0.039
tof_plot_cells_embedding	4.345	0.189	4.614
tof_plot_cells_layout	5.449	0.021	5.534
tof_plot_cells_scatter	0.002	0.001	0.003
tof_plot_clusters_heatmap	0.054	0.001	0.055
tof_plot_clusters_mst	0.205	0.002	0.212
tof_plot_clusters_volcano	0.034	0.001	0.035
tof_plot_model	0.633	0.010	0.657
tof_plot_sample_features	0.102	0.002	0.105
tof_plot_sample_heatmap	0.071	0.001	0.076
tof_postprocess	0.105	0.004	0.126
tof_predict	0.236	0.003	0.242
tof_preprocess	0.140	0.003	0.144
tof_read_data	0.089	0.004	0.097
tof_reduce_dimensions	2.877	0.056	3.011
tof_reduce_pca	0.162	0.002	0.170
tof_reduce_tsne	1.282	0.034	1.347
tof_reduce_umap	4.690	0.046	4.770
tof_set_panel	0.074	0.002	0.077
tof_spade_density	0.733	0.009	0.744
tof_split_data	0.050	0.002	0.052
tof_split_tidytof_reduced_dimensions	0.000	0.000	0.001
tof_train_model	1.435	0.019	1.463
tof_transform	0.134	0.002	0.137
tof_upsample	0.229	0.003	0.234
tof_upsample_distance	0.353	0.004	0.367
tof_upsample_neighbor	0.072	0.002	0.075
tof_write_data	0	0	0
tof_write_fcs	0.000	0.001	0.000
where	0.000	0.000	0.001