Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-10-03 11:50 -0400 (Thu, 03 Oct 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4461 |
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4716 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4466 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4498 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4446 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4445 |
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 2125/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
tidytof 0.99.8 (landing page) Timothy Keyes
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
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. |
Package: tidytof |
Version: 0.99.8 |
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_0.99.8.tar.gz |
StartedAt: 2024-10-03 10:08:30 -0000 (Thu, 03 Oct 2024) |
EndedAt: 2024-10-03 10:17:22 -0000 (Thu, 03 Oct 2024) |
EllapsedTime: 531.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: tidytof.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_0.99.8.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/tidytof.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14) GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (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 ‘0.99.8’ * 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: ‘g++ (GCC) 10.3.1’ * checking installed package size ... NOTE installed size is 5.5Mb sub-directories of 1Mb or more: help 2.1Mb libs 1.6Mb * 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 10.889 0.144 11.048 tof_plot_cells_layout 7.720 0.024 7.759 tof_cluster_flowsom 6.563 0.131 6.708 tof_plot_cells_embedding 6.334 0.008 6.350 * 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: 2 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/tidytof.Rcheck/00check.log’ for details.
tidytof.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL tidytof ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’ * installing *source* package ‘tidytof’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (GCC) 10.3.1’ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c code.cpp -o code.o g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.4.1/lib -L/usr/local/lib -o tidytof.so RcppExports.o code.o -L/home/biocbuild/R/R-4.4.1/lib -lR installing to /home/biocbuild/R/R-4.4.1/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)
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: 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 0.207 0.031 0.223
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: 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 0 | SKIP 0 | PASS 709 ] > > proc.time() user system elapsed 288.419 7.506 296.121
tidytof.Rcheck/tidytof-Ex.timings
name | user | system | elapsed | |
as_SingleCellExperiment | 0 | 0 | 0 | |
as_flowFrame | 0 | 0 | 0 | |
as_flowSet | 0 | 0 | 0 | |
as_seurat | 0 | 0 | 0 | |
as_tof_tbl | 0.061 | 0.008 | 0.071 | |
make_flowcore_annotated_data_frame | 0 | 0 | 0 | |
reexports | 0 | 0 | 0 | |
rev_asinh | 0.000 | 0.000 | 0.001 | |
tidytof_example_data | 0.003 | 0.000 | 0.003 | |
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 | 0 | 0 | |
tof_analyze_expression | 0 | 0 | 0 | |
tof_analyze_expression_diffcyt | 0 | 0 | 0 | |
tof_analyze_expression_lmm | 0 | 0 | 0 | |
tof_analyze_expression_ttest | 0 | 0 | 0 | |
tof_annotate_clusters | 0.126 | 0.008 | 0.134 | |
tof_apply_classifier | 0.001 | 0.000 | 0.000 | |
tof_assess_channels | 0.120 | 0.008 | 0.128 | |
tof_assess_clusters_distance | 0.551 | 0.076 | 0.628 | |
tof_assess_clusters_entropy | 0.995 | 0.000 | 0.997 | |
tof_assess_clusters_knn | 10.889 | 0.144 | 11.048 | |
tof_assess_flow_rate | 0.940 | 0.020 | 0.962 | |
tof_assess_flow_rate_tibble | 0.245 | 0.000 | 0.245 | |
tof_assess_model | 0.450 | 0.000 | 0.451 | |
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 | 0.016 | 0.000 | 0.016 | |
tof_cluster | 0.439 | 0.008 | 0.448 | |
tof_cluster_ddpr | 0.229 | 0.000 | 0.229 | |
tof_cluster_flowsom | 6.563 | 0.131 | 6.708 | |
tof_cluster_kmeans | 0.040 | 0.000 | 0.041 | |
tof_cluster_phenograph | 1.491 | 0.016 | 1.509 | |
tof_cosine_dist | 0 | 0 | 0 | |
tof_create_grid | 0.074 | 0.000 | 0.074 | |
tof_downsample | 0.215 | 0.000 | 0.215 | |
tof_downsample_constant | 0.085 | 0.008 | 0.093 | |
tof_downsample_density | 0.607 | 0.004 | 0.612 | |
tof_downsample_prop | 0.089 | 0.000 | 0.089 | |
tof_estimate_density | 0.399 | 0.004 | 0.404 | |
tof_extract_central_tendency | 0.232 | 0.000 | 0.233 | |
tof_extract_emd | 1.179 | 0.012 | 1.193 | |
tof_extract_features | 0.818 | 0.032 | 0.851 | |
tof_extract_jsd | 1.293 | 0.048 | 1.346 | |
tof_extract_proportion | 0.177 | 0.000 | 0.177 | |
tof_extract_threshold | 0.211 | 0.000 | 0.211 | |
tof_find_knn | 0.178 | 0.044 | 0.222 | |
tof_generate_palette | 0 | 0 | 0 | |
tof_get_model_mixture | 0.292 | 0.004 | 0.296 | |
tof_get_model_outcomes | 0.292 | 0.000 | 0.293 | |
tof_get_model_penalty | 0.274 | 0.000 | 0.275 | |
tof_get_model_training_data | 0.336 | 0.000 | 0.337 | |
tof_get_model_type | 0.276 | 0.000 | 0.277 | |
tof_get_model_x | 0.297 | 0.000 | 0.298 | |
tof_get_model_y | 0.298 | 0.000 | 0.300 | |
tof_get_panel | 0.046 | 0.004 | 0.050 | |
tof_log_rank_test | 0 | 0 | 0 | |
tof_make_knn_graph | 0 | 0 | 0 | |
tof_make_roc_curve | 0.428 | 0.000 | 0.429 | |
tof_metacluster | 1.002 | 0.012 | 1.015 | |
tof_metacluster_consensus | 0.418 | 0.000 | 0.419 | |
tof_metacluster_flowsom | 1.121 | 0.004 | 1.126 | |
tof_metacluster_hierarchical | 0.067 | 0.000 | 0.067 | |
tof_metacluster_kmeans | 0.07 | 0.00 | 0.07 | |
tof_metacluster_phenograph | 0.090 | 0.004 | 0.094 | |
tof_plot_cells_density | 0.045 | 0.000 | 0.045 | |
tof_plot_cells_embedding | 6.334 | 0.008 | 6.350 | |
tof_plot_cells_layout | 7.720 | 0.024 | 7.759 | |
tof_plot_cells_scatter | 0.004 | 0.000 | 0.003 | |
tof_plot_clusters_heatmap | 0.081 | 0.004 | 0.084 | |
tof_plot_clusters_mst | 0.283 | 0.008 | 0.291 | |
tof_plot_clusters_volcano | 0.044 | 0.004 | 0.048 | |
tof_plot_model | 0.860 | 0.008 | 0.870 | |
tof_plot_sample_features | 0.143 | 0.000 | 0.143 | |
tof_plot_sample_heatmap | 0.086 | 0.000 | 0.087 | |
tof_postprocess | 0.143 | 0.000 | 0.144 | |
tof_predict | 0.321 | 0.000 | 0.323 | |
tof_preprocess | 0.24 | 0.00 | 0.24 | |
tof_read_data | 0.116 | 0.003 | 0.120 | |
tof_reduce_dimensions | 3.055 | 0.016 | 3.073 | |
tof_reduce_pca | 0.224 | 0.000 | 0.224 | |
tof_reduce_tsne | 1.425 | 0.004 | 1.432 | |
tof_reduce_umap | 4.298 | 0.056 | 4.338 | |
tof_set_panel | 0.106 | 0.000 | 0.107 | |
tof_spade_density | 0.501 | 0.004 | 0.507 | |
tof_split_data | 0.061 | 0.000 | 0.061 | |
tof_split_tidytof_reduced_dimensions | 0 | 0 | 0 | |
tof_train_model | 2.372 | 0.020 | 2.397 | |
tof_transform | 0.207 | 0.000 | 0.208 | |
tof_upsample | 0.307 | 0.000 | 0.308 | |
tof_upsample_distance | 0.473 | 0.000 | 0.474 | |
tof_upsample_neighbor | 0.068 | 0.000 | 0.067 | |
tof_write_data | 0 | 0 | 0 | |
tof_write_fcs | 0 | 0 | 0 | |
where | 0 | 0 | 0 | |