Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-27 11:46 -0400 (Tue, 27 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4415 |
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 1838/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
scBubbletree 1.7.20 (landing page) Simo Kitanovski
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
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 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: 1.7.20 |
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_1.7.20.tar.gz |
StartedAt: 2024-08-27 00:04:51 -0400 (Tue, 27 Aug 2024) |
EndedAt: 2024-08-27 00:08:05 -0400 (Tue, 27 Aug 2024) |
EllapsedTime: 194.1 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_1.7.20.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/scBubbletree.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-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 Ventura 13.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘scBubbletree/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘scBubbletree’ version ‘1.7.20’ * 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 ‘lab_short’ get_dendrogram: no visible binding for global variable ‘lab_long’ get_dendrogram: no visible binding for global variable ‘label’ 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 6.990 0.124 7.117 get_r 6.336 0.422 6.762 * 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-3.20-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/4.4-arm64/Resources/library’ * installing *source* package ‘scBubbletree’ ... ** 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 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-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 99.261 4.912 104.232
scBubbletree.Rcheck/scBubbletree-Ex.timings
name | user | system | elapsed | |
d_500 | 0.002 | 0.000 | 0.003 | |
d_ccl | 0.007 | 0.001 | 0.008 | |
get_bubbletree_comparison | 6.990 | 0.124 | 7.117 | |
get_bubbletree_dummy | 2.321 | 0.038 | 2.359 | |
get_bubbletree_graph | 3.803 | 0.068 | 3.870 | |
get_bubbletree_kmeans | 4.386 | 0.058 | 4.444 | |
get_cat_tiles | 3.264 | 0.046 | 3.310 | |
get_gini | 0.001 | 0.000 | 0.000 | |
get_gini_k | 4.389 | 0.219 | 4.613 | |
get_k | 0.990 | 0.034 | 1.025 | |
get_num_cell_tiles | 4.394 | 0.057 | 4.451 | |
get_num_tiles | 4.350 | 0.050 | 4.402 | |
get_num_violins | 4.047 | 0.085 | 4.132 | |
get_r | 6.336 | 0.422 | 6.762 | |