Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-08-21 11:43 -0400 (Thu, 21 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4824 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4604 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4545 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4579 |
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 2209/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
tomoda 1.18.0 (landing page) Wendao Liu
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | 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 | OK | ||||||||||
To the developers/maintainers of the tomoda package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/tomoda.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: tomoda |
Version: 1.18.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:tomoda.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings tomoda_1.18.0.tar.gz |
StartedAt: 2025-08-19 14:59:33 -0000 (Tue, 19 Aug 2025) |
EndedAt: 2025-08-19 15:08:17 -0000 (Tue, 19 Aug 2025) |
EllapsedTime: 524.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: tomoda.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:tomoda.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings tomoda_1.18.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/tomoda.Rcheck’ * using R Under development (unstable) (2025-02-19 r87757) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘tomoda/DESCRIPTION’ ... OK * this is package ‘tomoda’ version ‘1.18.0’ * 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 ‘tomoda’ 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 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed findPeakGene 88.266 0.327 88.800 geneCorHeatmap 48.063 0.195 48.373 geneEmbedPlot 41.178 0.056 55.504 expHeatmap 37.726 0.292 38.104 corHeatmap 5.802 0.156 5.969 embedPlot 5.044 0.024 5.078 * 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: OK
tomoda.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL tomoda ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’ * installing *source* package ‘tomoda’ ... ** this is package ‘tomoda’ version ‘1.18.0’ ** using staged installation ** R ** data ** 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 (tomoda)
tomoda.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" Copyright (C) 2025 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. > library(testthat) > library(tomoda) > > test_check("tomoda") [ FAIL 0 | WARN 1 | SKIP 0 | PASS 43 ] [ FAIL 0 | WARN 1 | SKIP 0 | PASS 43 ] > > proc.time() user system elapsed 53.834 0.966 54.895
tomoda.Rcheck/tomoda-Ex.timings
name | user | system | elapsed | |
corHeatmap | 5.802 | 0.156 | 5.969 | |
createTomo | 2.419 | 0.079 | 2.504 | |
embedPlot | 5.044 | 0.024 | 5.078 | |
expHeatmap | 37.726 | 0.292 | 38.104 | |
findPeak | 0 | 0 | 0 | |
findPeakGene | 88.266 | 0.327 | 88.800 | |
geneCorHeatmap | 48.063 | 0.195 | 48.373 | |
geneEmbedPlot | 41.178 | 0.056 | 55.504 | |
hierarchClust | 1.849 | 0.000 | 1.854 | |
kmeansClust | 1.742 | 0.024 | 3.000 | |
linePlot | 2.330 | 0.016 | 4.704 | |
normalizeTomo | 0.271 | 0.000 | 0.545 | |
runPCA | 2.218 | 0.024 | 4.497 | |
runTSNE | 2.034 | 0.012 | 2.679 | |
runUMAP | 2.671 | 0.016 | 2.793 | |
scaleTomo | 0.844 | 0.000 | 0.846 | |
tomoMatrix | 0.830 | 0.004 | 0.837 | |
tomoSummarizedExperiment | 0.854 | 0.000 | 0.857 | |