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This page was generated on 2025-10-18 12:08 -0400 (Sat, 18 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4887
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4677
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4622
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4632
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 2224/2353HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
tomoda 1.19.0  (landing page)
Wendao Liu
Snapshot Date: 2025-10-17 13:45 -0400 (Fri, 17 Oct 2025)
git_url: https://git.bioconductor.org/packages/tomoda
git_branch: devel
git_last_commit: 487041e
git_last_commit_date: 2025-04-15 12:10:52 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for tomoda on taishan

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.

raw results


Summary

Package: tomoda
Version: 1.19.0
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_1.19.0.tar.gz
StartedAt: 2025-10-17 14:33:19 -0000 (Fri, 17 Oct 2025)
EndedAt: 2025-10-17 14:42:15 -0000 (Fri, 17 Oct 2025)
EllapsedTime: 535.5 seconds
RetCode: 0
Status:   OK  
CheckDir: tomoda.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/tomoda.Rcheck’
* using R version 4.5.0 (2025-04-11)
* 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)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘tomoda/DESCRIPTION’ ... OK
* this is package ‘tomoda’ version ‘1.19.0’
* 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   76.299  0.643  82.253
geneCorHeatmap 41.376  0.203  43.762
geneEmbedPlot  36.969  0.099  50.056
expHeatmap     33.197  0.557  35.380
runUMAP         1.900  8.644  24.584
corHeatmap      6.334  0.736   8.224
embedPlot       5.029  0.025   5.169
* 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


Installation output

tomoda.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL tomoda
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘tomoda’ ...
** this is package ‘tomoda’ version ‘1.19.0’
** 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)

Tests output

tomoda.Rcheck/tests/testthat.Rout


R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
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 
 48.410   0.893  58.792 

Example timings

tomoda.Rcheck/tomoda-Ex.timings

nameusersystemelapsed
corHeatmap6.3340.7368.224
createTomo2.2120.1082.400
embedPlot5.0290.0255.169
expHeatmap33.197 0.55735.380
findPeak000
findPeakGene76.299 0.64382.253
geneCorHeatmap41.376 0.20343.762
geneEmbedPlot36.969 0.09950.056
hierarchClust1.9080.0161.943
kmeansClust1.6680.0002.457
linePlot2.9920.0044.894
normalizeTomo0.2500.0000.611
runPCA1.4770.0073.279
runTSNE2.2710.0684.185
runUMAP 1.900 8.64424.584
scaleTomo0.7880.0520.859
tomoMatrix0.8670.0430.917
tomoSummarizedExperiment0.8400.0120.865