Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-07-24 11:46 -0400 (Thu, 24 Jul 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4821 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4563 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4601 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4542 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4578 |
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 1894/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
scBubbletree 1.10.0 (landing page) Simo Kitanovski
| nebbiolo1 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | NA | ||||||||||
To the developers/maintainers of the scBubbletree package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scBubbletree.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: scBubbletree |
Version: 1.10.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scBubbletree.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scBubbletree_1.10.0.tar.gz |
StartedAt: 2025-07-22 09:55:05 -0400 (Tue, 22 Jul 2025) |
EndedAt: 2025-07-22 10:11:33 -0400 (Tue, 22 Jul 2025) |
EllapsedTime: 987.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: scBubbletree.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scBubbletree.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scBubbletree_1.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/scBubbletree.Rcheck’ * using R version 4.5.1 RC (2025-06-05 r88288) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘scBubbletree/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘scBubbletree’ version ‘1.10.0’ * 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 ‘scBubbletree’ can be installed ... OK * 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 ... NOTE Namespace in Imports field not imported from: ‘base’ All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE compare_bubbletrees: no visible binding for global variable ‘isTip’ compare_bubbletrees: no visible binding for global variable ‘Cells’ compare_bubbletrees: no visible binding for global variable ‘lab_short’ compare_bubbletrees: no visible binding for global variable ‘label’ compare_bubbletrees: no visible binding for global variable ‘JD’ compare_bubbletrees: no visible binding for global variable ‘intersection’ get_dendrogram: no visible binding for global variable ‘isTip’ get_dendrogram: no visible binding for global variable ‘Cells’ get_dendrogram: no visible binding for global variable ‘label’ get_dendrogram: no visible binding for global variable ‘lab_short’ get_dendrogram: no visible binding for global variable ‘lab_long’ get_num_cell_tiles: no visible binding for global variable ‘cluster’ ggplot_cat_tiles: no visible binding for global variable ‘feature’ ggplot_cat_tiles: no visible binding for global variable ‘cluster’ ggplot_cat_tiles: no visible binding for global variable ‘percent’ ggplot_num_cell_tiles: no visible binding for global variable ‘cluster’ ggplot_num_cell_tiles: no visible binding for global variable ‘f’ ggplot_num_tiles: no visible binding for global variable ‘feature’ ggplot_num_tiles: no visible binding for global variable ‘cluster’ ggplot_num_tiles: no visible binding for global variable ‘value’ ggplot_num_violins: no visible binding for global variable ‘cluster’ ggplot_num_violins: no visible binding for global variable ‘value’ Undefined global functions or variables: Cells JD cluster f feature intersection isTip lab_long lab_short label percent value * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed get_bubbletree_comparison 30.731 0.326 44.446 get_num_cell_tiles 22.125 0.235 24.803 get_num_tiles 21.663 0.198 22.583 get_bubbletree_kmeans 20.265 0.108 23.988 get_r 17.097 0.493 17.590 get_bubbletree_graph 17.243 0.150 17.396 get_num_violins 15.745 0.162 16.611 get_cat_tiles 14.267 0.145 17.784 get_gini_k 10.751 0.397 11.157 get_bubbletree_dummy 9.859 0.125 9.985 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... 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 ‘/Users/biocbuild/bbs-3.21-bioc/meat/scBubbletree.Rcheck/00check.log’ for details.
scBubbletree.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL scBubbletree ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘scBubbletree’ ... ** this is package ‘scBubbletree’ version ‘1.10.0’ ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (scBubbletree)
scBubbletree.Rcheck/tests/testthat.Rout
R version 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" Copyright (C) 2025 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. > library(testthat) > library(scBubbletree) > > test_check("scBubbletree") Tests input rules of get_bubbletree_graph Tests input rules of get_bubbletree_kmeans Tests input rules of get_cat_tiles Tests input rules of get_gini_k Tests input rules of get_gini Tests input rules of get_k Tests input rules of get_num_tiles Tests input rules of get_num_violins Tests input rules of get_r Tests input rules of util [ FAIL 0 | WARN 0 | SKIP 0 | PASS 477 ] > > proc.time() user system elapsed 340.687 8.892 352.403
scBubbletree.Rcheck/scBubbletree-Ex.timings
name | user | system | elapsed | |
d_500 | 0.005 | 0.002 | 0.007 | |
d_ccl | 0.016 | 0.002 | 0.018 | |
get_bubbletree_comparison | 30.731 | 0.326 | 44.446 | |
get_bubbletree_dummy | 9.859 | 0.125 | 9.985 | |
get_bubbletree_graph | 17.243 | 0.150 | 17.396 | |
get_bubbletree_kmeans | 20.265 | 0.108 | 23.988 | |
get_cat_tiles | 14.267 | 0.145 | 17.784 | |
get_gini | 0.002 | 0.001 | 0.003 | |
get_gini_k | 10.751 | 0.397 | 11.157 | |
get_k | 2.691 | 0.178 | 3.854 | |
get_num_cell_tiles | 22.125 | 0.235 | 24.803 | |
get_num_tiles | 21.663 | 0.198 | 22.583 | |
get_num_violins | 15.745 | 0.162 | 16.611 | |
get_r | 17.097 | 0.493 | 17.590 | |