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This page was generated on 2025-08-26 12:07 -0400 (Tue, 26 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4821
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4610
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4553
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4539
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 67/2319HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
animalcules 1.25.0  (landing page)
Jessica McClintock
Snapshot Date: 2025-08-25 13:45 -0400 (Mon, 25 Aug 2025)
git_url: https://git.bioconductor.org/packages/animalcules
git_branch: devel
git_last_commit: b955827
git_last_commit_date: 2025-06-05 16:39:52 -0400 (Thu, 05 Jun 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 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 animalcules on taishan

To the developers/maintainers of the animalcules package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/animalcules.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: animalcules
Version: 1.25.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:animalcules.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings animalcules_1.25.0.tar.gz
StartedAt: 2025-08-26 04:30:07 -0000 (Tue, 26 Aug 2025)
EndedAt: 2025-08-26 04:37:07 -0000 (Tue, 26 Aug 2025)
EllapsedTime: 419.8 seconds
RetCode: 0
Status:   OK  
CheckDir: animalcules.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:animalcules.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings animalcules_1.25.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/animalcules.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 ‘animalcules/DESCRIPTION’ ... OK
* this is package ‘animalcules’ version ‘1.25.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 31 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ‘animalcules’ 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
dimred_tsne            8.574  0.182  10.249
find_biomarker         5.683  0.104   6.780
differential_abundance 5.457  0.216  10.503
* 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

animalcules.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘animalcules’ ...
** this is package ‘animalcules’ version ‘1.25.0’
** using staged installation
** R
** 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 (animalcules)

Tests output

animalcules.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(animalcules)
> 
> test_check("animalcules")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 38 ]
> 
> proc.time()
   user  system elapsed 
 35.650   1.284  43.796 

Example timings

animalcules.Rcheck/animalcules-Ex.timings

nameusersystemelapsed
alpha_div_boxplot0.6790.0560.851
alpha_div_test0.0040.0000.008
counts_to_logcpm0.0020.0000.007
counts_to_relabu0.0030.0000.003
df_char_to_factor0.0010.0000.000
differential_abundance 5.457 0.21610.503
dimred_pca0.2140.0080.402
dimred_pcoa0.1540.0080.162
dimred_tsne 8.574 0.18210.249
dimred_umap0.4790.0040.572
diversities0.0010.0000.000
diversities_help0.0010.0000.000
diversity_beta_boxplot0.2730.0320.305
diversity_beta_heatmap0.2540.0040.258
diversity_beta_test0.2110.0000.211
do_alpha_div_test0.0580.0000.059
filter_categorize0.3900.0200.745
filter_summary_bar_density0.3670.0040.751
filter_summary_pie_box0.2940.0000.587
find_biomarker5.6830.1046.780
find_taxon_mat0.2330.0284.921
find_taxonomy0.0380.0001.288
find_taxonomy_3000.0340.0010.785
gini_simpson0.0010.0000.000
grep_tid000
inverse_simpson000
is_categorical000
is_integer0000
is_integer10.0000.0000.001
mae_pick_organisms0.1500.0040.307
mae_pick_samples0.1600.0030.237
pct2str000
percent000
relabu_barplot1.3830.0111.641
relabu_boxplot0.1190.0120.130
relabu_heatmap0.1580.0040.162
run_animalcules000
shannon000
simpson_index000
upsample_counts0.0120.0040.016