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This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 2147/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
tidytof 1.0.0  (landing page)
Timothy Keyes
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/tidytof
git_branch: RELEASE_3_20
git_last_commit: 953e93b
git_last_commit_date: 2024-10-29 11:33:26 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for tidytof on merida1

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: 2024-12-20 10:44:55 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 10:57:55 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 779.1 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 4.4.2 (2024-10-31)
* using platform: x86_64-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 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 ‘1.0.0’
* 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 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  18.187  0.094  18.565
tof_cluster_flowsom       9.086  1.232  10.477
tof_plot_cells_layout     6.385  0.027   6.573
tof_plot_cells_embedding  5.373  0.146   5.682
* 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-x86_64/Resources/library’
* installing *source* package ‘tidytof’ ...
** 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/4.4-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/4.4-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 -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 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 
  0.357   0.117   0.441 

tidytof.Rcheck/tests/testthat.Rout


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 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 0 | WARN 0 | SKIP 0 | PASS 709 ]
> 
> proc.time()
   user  system elapsed 
379.805   9.551 396.258 

Example timings

tidytof.Rcheck/tidytof-Ex.timings

nameusersystemelapsed
as_SingleCellExperiment0.0000.0010.001
as_flowFrame0.0010.0000.001
as_flowSet0.0000.0010.001
as_seurat0.0010.0010.001
as_tof_tbl0.1040.0130.118
make_flowcore_annotated_data_frame000
reexports000
rev_asinh0.0000.0010.001
tidytof_example_data0.0040.0020.005
tof_analyze_abundance0.0000.0010.001
tof_analyze_abundance_diffcyt0.0000.0010.001
tof_analyze_abundance_glmm000
tof_analyze_abundance_ttest0.0010.0000.000
tof_analyze_expression0.0000.0000.001
tof_analyze_expression_diffcyt0.0000.0010.000
tof_analyze_expression_lmm0.0000.0010.000
tof_analyze_expression_ttest0.0000.0010.000
tof_annotate_clusters0.2010.0290.230
tof_apply_classifier0.0000.0010.001
tof_assess_channels0.1670.0210.188
tof_assess_clusters_distance1.0070.1031.117
tof_assess_clusters_entropy1.9050.0131.944
tof_assess_clusters_knn18.187 0.09418.565
tof_assess_flow_rate1.5470.0131.563
tof_assess_flow_rate_tibble0.3890.0030.393
tof_assess_model0.6890.0080.699
tof_batch_correct0.0000.0010.001
tof_batch_correct_quantile000
tof_batch_correct_quantile_tibble000
tof_batch_correct_rescale0.0000.0000.001
tof_calculate_flow_rate0.0260.0020.028
tof_cluster0.8710.0270.900
tof_cluster_ddpr0.4020.0050.415
tof_cluster_flowsom 9.086 1.23210.477
tof_cluster_kmeans0.0600.0010.061
tof_cluster_phenograph2.9530.0653.056
tof_cosine_dist0.0000.0010.001
tof_create_grid0.1040.0010.106
tof_downsample0.3340.0030.340
tof_downsample_constant0.1370.0010.138
tof_downsample_density0.9290.0040.936
tof_downsample_prop0.1440.0020.146
tof_estimate_density0.6260.0130.649
tof_extract_central_tendency0.3690.0020.375
tof_extract_emd1.8680.0811.979
tof_extract_features1.2180.0191.245
tof_extract_jsd2.0040.1562.188
tof_extract_proportion0.2650.0020.268
tof_extract_threshold0.3410.0030.353
tof_find_knn0.3980.5640.970
tof_generate_palette0.0010.0010.000
tof_get_model_mixture0.4650.0030.470
tof_get_model_outcomes0.4580.0020.463
tof_get_model_penalty0.4640.0070.475
tof_get_model_training_data0.5140.0030.524
tof_get_model_type0.4510.0030.454
tof_get_model_x0.4590.0080.471
tof_get_model_y0.4570.0040.468
tof_get_panel0.0840.0030.090
tof_log_rank_test0.0000.0000.001
tof_make_knn_graph000
tof_make_roc_curve0.6490.0040.656
tof_metacluster1.6910.0751.791
tof_metacluster_consensus0.6750.0250.733
tof_metacluster_flowsom1.7740.0681.866
tof_metacluster_hierarchical0.1090.0020.110
tof_metacluster_kmeans0.1200.0010.123
tof_metacluster_phenograph0.1520.0010.155
tof_plot_cells_density0.0700.0010.070
tof_plot_cells_embedding5.3730.1465.682
tof_plot_cells_layout6.3850.0276.573
tof_plot_cells_scatter0.0050.0010.006
tof_plot_clusters_heatmap0.1240.0020.153
tof_plot_clusters_mst0.4170.0060.434
tof_plot_clusters_volcano0.0660.0010.103
tof_plot_model1.1730.0171.200
tof_plot_sample_features0.2340.0030.249
tof_plot_sample_heatmap0.1070.0010.110
tof_postprocess0.2180.0040.232
tof_predict0.5010.0040.576
tof_preprocess0.3550.0050.386
tof_read_data0.1670.0030.180
tof_reduce_dimensions3.5960.1184.159
tof_reduce_pca0.3230.0030.342
tof_reduce_tsne1.5370.0291.660
tof_reduce_umap4.2740.0584.564
tof_set_panel0.1660.0040.173
tof_spade_density0.7800.0050.888
tof_split_data0.0990.0040.115
tof_split_tidytof_reduced_dimensions0.0000.0000.001
tof_train_model3.1420.0273.584
tof_transform0.3260.0040.352
tof_upsample0.5230.0040.531
tof_upsample_distance1.1980.0091.213
tof_upsample_neighbor0.1050.0030.108
tof_write_data0.0010.0000.001
tof_write_fcs0.0000.0010.000
where0.0010.0000.001