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This page was generated on 2024-11-20 12:07 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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: 2024-11-19 13:40 -0500 (Tue, 19 Nov 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)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


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: 1.0.0
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: 2024-11-20 03:25:09 -0500 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 03:33:56 -0500 (Wed, 20 Nov 2024)
EllapsedTime: 527.4 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 4.4.1 (2024-06-14)
* 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 ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 6.165  0.052   6.245
* 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 4.4.1 (2024-06-14) -- "Race for Your Life"
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 
  0.180   0.072   0.250 

tidytof.Rcheck/tests/testthat.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
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 
147.190   4.987 150.296 

Example timings

tidytof.Rcheck/tidytof-Ex.timings

nameusersystemelapsed
as_SingleCellExperiment000
as_flowFrame0.0000.0010.000
as_flowSet0.0000.0000.001
as_seurat0.0000.0000.001
as_tof_tbl0.0460.0040.051
make_flowcore_annotated_data_frame000
reexports000
rev_asinh000
tidytof_example_data0.0020.0010.003
tof_analyze_abundance0.0000.0000.001
tof_analyze_abundance_diffcyt000
tof_analyze_abundance_glmm000
tof_analyze_abundance_ttest0.0000.0010.000
tof_analyze_expression000
tof_analyze_expression_diffcyt000
tof_analyze_expression_lmm0.0000.0000.001
tof_analyze_expression_ttest000
tof_annotate_clusters0.0810.0090.090
tof_apply_classifier000
tof_assess_channels0.0700.0050.075
tof_assess_clusters_distance0.3540.0290.384
tof_assess_clusters_entropy0.5190.0050.526
tof_assess_clusters_knn6.1650.0526.245
tof_assess_flow_rate0.5430.0080.554
tof_assess_flow_rate_tibble0.1390.0020.142
tof_assess_model0.2680.0050.275
tof_batch_correct0.0000.0000.001
tof_batch_correct_quantile000
tof_batch_correct_quantile_tibble000
tof_batch_correct_rescale000
tof_calculate_flow_rate0.0110.0010.012
tof_cluster0.4000.0100.414
tof_cluster_ddpr0.1390.0020.141
tof_cluster_flowsom3.8470.5884.478
tof_cluster_kmeans0.0280.0010.030
tof_cluster_phenograph1.4060.0561.470
tof_cosine_dist000
tof_create_grid0.0410.0000.042
tof_downsample0.1330.0010.134
tof_downsample_constant0.0760.0080.085
tof_downsample_density0.4630.0040.469
tof_downsample_prop0.0550.0000.055
tof_estimate_density0.3180.0030.323
tof_extract_central_tendency0.1620.0100.173
tof_extract_emd1.0250.0861.128
tof_extract_features0.4880.0100.501
tof_extract_jsd0.8260.1070.965
tof_extract_proportion0.0990.0010.100
tof_extract_threshold0.1280.0000.129
tof_find_knn0.1680.1460.315
tof_generate_palette000
tof_get_model_mixture0.1750.0010.177
tof_get_model_outcomes0.1570.0010.158
tof_get_model_penalty0.1650.0020.166
tof_get_model_training_data0.1810.0000.182
tof_get_model_type0.1610.0000.163
tof_get_model_x0.1700.0020.172
tof_get_model_y0.1650.0010.166
tof_get_panel0.0310.0010.032
tof_log_rank_test000
tof_make_knn_graph000
tof_make_roc_curve0.2330.0010.234
tof_metacluster0.5150.0400.562
tof_metacluster_consensus0.2290.0190.253
tof_metacluster_flowsom0.5230.0570.586
tof_metacluster_hierarchical0.0390.0000.040
tof_metacluster_kmeans0.040.000.04
tof_metacluster_phenograph0.0550.0010.055
tof_plot_cells_density0.0250.0000.025
tof_plot_cells_embedding2.2700.0992.399
tof_plot_cells_layout2.7930.0072.807
tof_plot_cells_scatter0.0020.0000.002
tof_plot_clusters_heatmap0.0430.0000.043
tof_plot_clusters_mst0.1550.0010.157
tof_plot_clusters_volcano0.0250.0000.025
tof_plot_model0.4530.0070.462
tof_plot_sample_features0.0740.0000.074
tof_plot_sample_heatmap0.0470.0000.048
tof_postprocess0.0810.0020.083
tof_predict0.1910.0020.195
tof_preprocess0.1310.0020.133
tof_read_data0.0620.0010.063
tof_reduce_dimensions1.8040.0421.846
tof_reduce_pca0.1190.0010.120
tof_reduce_tsne0.6610.0260.690
tof_reduce_umap2.8130.0472.830
tof_set_panel0.0700.0020.073
tof_spade_density0.4410.0030.446
tof_split_data0.0440.0020.046
tof_split_tidytof_reduced_dimensions000
tof_train_model1.1100.0141.128
tof_transform0.1250.0010.127
tof_upsample0.1800.0020.184
tof_upsample_distance0.3210.0040.327
tof_upsample_neighbor0.0520.0010.054
tof_write_data000
tof_write_fcs0.0010.0000.000
where000