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This page was generated on 2025-10-13 11:42 -0400 (Mon, 13 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4833
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4614
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4555
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4586
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: 2025-10-09 13:40 -0400 (Thu, 09 Oct 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    OK    OK  


CHECK results for tidytof on kunpeng2

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: tidytof
Version: 1.2.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:tidytof.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings tidytof_1.2.0.tar.gz
StartedAt: 2025-10-10 14:52:02 -0000 (Fri, 10 Oct 2025)
EndedAt: 2025-10-10 15:01:25 -0000 (Fri, 10 Oct 2025)
EllapsedTime: 562.7 seconds
RetCode: 0
Status:   OK  
CheckDir: tidytof.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:tidytof.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings tidytof_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/tidytof.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* 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: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
* checking installed package size ... INFO
  installed size is  5.2Mb
  sub-directories of 1Mb or more:
    help   2.1Mb
    libs   1.3Mb
* 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 loading without being on the library search path ... 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  12.679  0.164  12.871
tof_plot_cells_layout     7.661  0.024   7.696
tof_cluster_flowsom       7.030  0.156   7.206
tof_plot_cells_embedding  6.791  0.016   6.827
* 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
  ‘/home/biocbuild/bbs-3.21-bioc/meat/tidytof.Rcheck/00check.log’
for details.


Installation output

tidytof.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL tidytof
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘tidytof’ ...
** this is package ‘tidytof’ version ‘1.2.0’
** using staged installation
** libs
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c code.cpp -o code.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o tidytof.so RcppExports.o code.o -L/home/biocbuild/R/R/lib -lR
installing to /home/biocbuild/R/R-devel_2025-02-19/site-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 Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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 
  0.198   0.023   0.208 

tidytof.Rcheck/tests/testthat.Rout


R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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 1 | SKIP 0 | PASS 709 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 709 ]
> 
> proc.time()
   user  system elapsed 
302.530   6.368 308.105 

Example timings

tidytof.Rcheck/tidytof-Ex.timings

nameusersystemelapsed
as_SingleCellExperiment0.0000.0000.001
as_flowFrame000
as_flowSet000
as_seurat0.0000.0000.001
as_tof_tbl0.0720.0000.073
make_flowcore_annotated_data_frame000
reexports000
rev_asinh0.0000.0010.000
tidytof_example_data0.0000.0030.002
tof_analyze_abundance000
tof_analyze_abundance_diffcyt000
tof_analyze_abundance_glmm0.0000.0010.000
tof_analyze_abundance_ttest000
tof_analyze_expression000
tof_analyze_expression_diffcyt000
tof_analyze_expression_lmm000
tof_analyze_expression_ttest000
tof_annotate_clusters0.5520.0230.576
tof_apply_classifier000
tof_assess_channels0.1190.0000.120
tof_assess_clusters_distance0.6050.0600.666
tof_assess_clusters_entropy1.0610.0671.131
tof_assess_clusters_knn12.679 0.16412.871
tof_assess_flow_rate1.4720.0361.511
tof_assess_flow_rate_tibble0.4270.0000.428
tof_assess_model0.5910.0040.596
tof_batch_correct000
tof_batch_correct_quantile000
tof_batch_correct_quantile_tibble000
tof_batch_correct_rescale000
tof_calculate_flow_rate0.0180.0000.017
tof_cluster0.4890.0000.490
tof_cluster_ddpr0.2530.0000.254
tof_cluster_flowsom7.0300.1567.206
tof_cluster_kmeans0.0450.0000.046
tof_cluster_phenograph1.4960.0041.503
tof_cosine_dist000
tof_create_grid0.0670.0040.072
tof_downsample0.2280.0040.233
tof_downsample_constant0.1210.0000.121
tof_downsample_density0.6210.0000.623
tof_downsample_prop0.1020.0000.101
tof_estimate_density0.3950.0000.396
tof_extract_central_tendency0.250.000.25
tof_extract_emd0.6630.0040.669
tof_extract_features0.7690.0000.771
tof_extract_jsd0.7730.0320.809
tof_extract_proportion0.1910.0000.192
tof_extract_threshold0.2280.0000.228
tof_find_knn0.1830.0190.202
tof_generate_palette000
tof_get_model_mixture0.3020.0010.303
tof_get_model_outcomes0.3010.0000.302
tof_get_model_penalty0.3230.0000.323
tof_get_model_training_data0.3640.0000.365
tof_get_model_type0.3260.0000.326
tof_get_model_x0.3320.0000.333
tof_get_model_y0.3160.0000.317
tof_get_panel0.0500.0000.051
tof_log_rank_test0.0000.0000.001
tof_make_knn_graph000
tof_make_roc_curve0.4530.0000.453
tof_metacluster1.0040.0071.015
tof_metacluster_consensus0.4360.0000.437
tof_metacluster_flowsom1.0520.0121.067
tof_metacluster_hierarchical0.0740.0000.074
tof_metacluster_kmeans0.0760.0000.077
tof_metacluster_phenograph0.0950.0000.095
tof_plot_cells_density0.1060.0000.106
tof_plot_cells_embedding6.7910.0166.827
tof_plot_cells_layout7.6610.0247.696
tof_plot_cells_scatter0.0030.0000.004
tof_plot_clusters_heatmap0.1660.0080.176
tof_plot_clusters_mst0.3780.0240.403
tof_plot_clusters_volcano0.1200.0040.123
tof_plot_model0.9480.0040.954
tof_plot_sample_features0.2370.0000.238
tof_plot_sample_heatmap0.1450.0000.145
tof_postprocess0.1380.0000.138
tof_predict0.3240.0000.325
tof_preprocess0.2230.0000.223
tof_read_data0.1020.0000.103
tof_reduce_dimensions3.0400.0403.097
tof_reduce_pca0.2070.0000.208
tof_reduce_tsne1.3680.0001.370
tof_reduce_umap4.4550.0044.464
tof_set_panel0.1060.0000.106
tof_spade_density0.4970.0080.506
tof_split_data0.070.000.07
tof_split_tidytof_reduced_dimensions000
tof_train_model1.9510.0592.013
tof_transform0.2200.0200.241
tof_upsample0.3290.0120.342
tof_upsample_distance0.4980.0240.523
tof_upsample_neighbor0.0670.0040.070
tof_write_data000
tof_write_fcs000
where000