Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-20 12:03 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (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 2147/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
tidytof 1.0.0 (landing page) Timothy Keyes
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | 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. |
Package: tidytof |
Version: 1.0.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:tidytof.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings tidytof_1.0.0.tar.gz |
StartedAt: 2024-11-20 10:45:03 -0500 (Wed, 20 Nov 2024) |
EndedAt: 2024-11-20 10:53:25 -0500 (Wed, 20 Nov 2024) |
EllapsedTime: 502.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: tidytof.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:tidytof.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings tidytof_1.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/tidytof.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * 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: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ * checking installed package size ... NOTE installed size is 5.2Mb sub-directories of 1Mb or more: help 2.2Mb libs 1.2Mb * 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 5.548 0.004 5.558 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/tidytof.Rcheck/00check.log’ for details.
tidytof.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL tidytof ### ############################################################################## ############################################################################## * installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘tidytof’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/include" -DNDEBUG -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/lib -L/usr/local/lib -o tidytof.so RcppExports.o code.o -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR installing to /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/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 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-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 0.102 0.044 0.149
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-pc-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 151.918 1.950 152.752
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 | 0.035 | 0.002 | 0.037 | |
make_flowcore_annotated_data_frame | 0.001 | 0.000 | 0.000 | |
reexports | 0 | 0 | 0 | |
rev_asinh | 0.000 | 0.000 | 0.001 | |
tidytof_example_data | 0.000 | 0.001 | 0.001 | |
tof_analyze_abundance | 0 | 0 | 0 | |
tof_analyze_abundance_diffcyt | 0 | 0 | 0 | |
tof_analyze_abundance_glmm | 0 | 0 | 0 | |
tof_analyze_abundance_ttest | 0 | 0 | 0 | |
tof_analyze_expression | 0.000 | 0.000 | 0.001 | |
tof_analyze_expression_diffcyt | 0 | 0 | 0 | |
tof_analyze_expression_lmm | 0 | 0 | 0 | |
tof_analyze_expression_ttest | 0 | 0 | 0 | |
tof_annotate_clusters | 0.060 | 0.016 | 0.076 | |
tof_apply_classifier | 0 | 0 | 0 | |
tof_assess_channels | 0.050 | 0.014 | 0.064 | |
tof_assess_clusters_distance | 0.272 | 0.057 | 0.329 | |
tof_assess_clusters_entropy | 0.452 | 0.001 | 0.453 | |
tof_assess_clusters_knn | 5.548 | 0.004 | 5.558 | |
tof_assess_flow_rate | 0.448 | 0.002 | 0.451 | |
tof_assess_flow_rate_tibble | 0.114 | 0.000 | 0.113 | |
tof_assess_model | 0.209 | 0.000 | 0.209 | |
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 | 0.007 | 0.000 | 0.008 | |
tof_cluster | 0.251 | 0.014 | 0.265 | |
tof_cluster_ddpr | 0.108 | 0.002 | 0.109 | |
tof_cluster_flowsom | 3.084 | 0.071 | 3.162 | |
tof_cluster_kmeans | 0.021 | 0.000 | 0.022 | |
tof_cluster_phenograph | 0.825 | 0.000 | 0.824 | |
tof_cosine_dist | 0 | 0 | 0 | |
tof_create_grid | 0.031 | 0.000 | 0.031 | |
tof_downsample | 0.097 | 0.000 | 0.097 | |
tof_downsample_constant | 0.04 | 0.00 | 0.04 | |
tof_downsample_density | 0.382 | 0.008 | 0.389 | |
tof_downsample_prop | 0.049 | 0.004 | 0.053 | |
tof_estimate_density | 0.265 | 0.007 | 0.273 | |
tof_extract_central_tendency | 0.11 | 0.00 | 0.11 | |
tof_extract_emd | 0.573 | 0.026 | 0.600 | |
tof_extract_features | 0.374 | 0.003 | 0.378 | |
tof_extract_jsd | 0.627 | 0.027 | 0.655 | |
tof_extract_proportion | 0.088 | 0.000 | 0.088 | |
tof_extract_threshold | 0.095 | 0.000 | 0.096 | |
tof_find_knn | 0.131 | 0.059 | 0.190 | |
tof_generate_palette | 0.001 | 0.000 | 0.000 | |
tof_get_model_mixture | 0.137 | 0.000 | 0.137 | |
tof_get_model_outcomes | 0.139 | 0.001 | 0.140 | |
tof_get_model_penalty | 0.13 | 0.00 | 0.13 | |
tof_get_model_training_data | 0.162 | 0.000 | 0.161 | |
tof_get_model_type | 0.127 | 0.001 | 0.128 | |
tof_get_model_x | 0.135 | 0.001 | 0.136 | |
tof_get_model_y | 0.142 | 0.000 | 0.142 | |
tof_get_panel | 0.025 | 0.000 | 0.025 | |
tof_log_rank_test | 0 | 0 | 0 | |
tof_make_knn_graph | 0 | 0 | 0 | |
tof_make_roc_curve | 0.189 | 0.000 | 0.190 | |
tof_metacluster | 0.470 | 0.008 | 0.479 | |
tof_metacluster_consensus | 0.197 | 0.001 | 0.199 | |
tof_metacluster_flowsom | 0.495 | 0.003 | 0.499 | |
tof_metacluster_hierarchical | 0.033 | 0.000 | 0.033 | |
tof_metacluster_kmeans | 0.031 | 0.000 | 0.032 | |
tof_metacluster_phenograph | 0.043 | 0.000 | 0.043 | |
tof_plot_cells_density | 0.022 | 0.000 | 0.022 | |
tof_plot_cells_embedding | 2.258 | 0.003 | 2.262 | |
tof_plot_cells_layout | 2.180 | 0.005 | 2.186 | |
tof_plot_cells_scatter | 0.002 | 0.000 | 0.002 | |
tof_plot_clusters_heatmap | 0.037 | 0.000 | 0.037 | |
tof_plot_clusters_mst | 0.135 | 0.001 | 0.136 | |
tof_plot_clusters_volcano | 0.02 | 0.00 | 0.02 | |
tof_plot_model | 0.364 | 0.001 | 0.365 | |
tof_plot_sample_features | 0.061 | 0.001 | 0.062 | |
tof_plot_sample_heatmap | 0.031 | 0.000 | 0.031 | |
tof_postprocess | 0.065 | 0.000 | 0.065 | |
tof_predict | 0.156 | 0.000 | 0.156 | |
tof_preprocess | 0.099 | 0.001 | 0.100 | |
tof_read_data | 0.051 | 0.000 | 0.051 | |
tof_reduce_dimensions | 1.824 | 0.011 | 1.841 | |
tof_reduce_pca | 0.094 | 0.000 | 0.094 | |
tof_reduce_tsne | 0.595 | 0.002 | 0.597 | |
tof_reduce_umap | 2.963 | 0.013 | 2.963 | |
tof_set_panel | 0.052 | 0.000 | 0.052 | |
tof_spade_density | 0.365 | 0.006 | 0.371 | |
tof_split_data | 0.029 | 0.000 | 0.029 | |
tof_split_tidytof_reduced_dimensions | 0 | 0 | 0 | |
tof_train_model | 1.256 | 0.003 | 1.260 | |
tof_transform | 0.098 | 0.000 | 0.098 | |
tof_upsample | 0.148 | 0.000 | 0.148 | |
tof_upsample_distance | 0.222 | 0.001 | 0.223 | |
tof_upsample_neighbor | 0.038 | 0.000 | 0.037 | |
tof_write_data | 0 | 0 | 0 | |
tof_write_fcs | 0 | 0 | 0 | |
where | 0 | 0 | 0 | |