Francesc Catala-Moll
| Snapshot Date: 2026-04-23 13:40 -0400 (Thu, 23 Apr 2026) |
| git_url: https://git.bioconductor.org/packages/dar |
| git_branch: devel |
| git_last_commit: b512d65 |
| git_last_commit_date: 2026-04-22 16:03:19 -0400 (Wed, 22 Apr 2026) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-04-24 11:35 -0400 (Fri, 24 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4958 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 alpha (2026-04-08 r89818) | 4705 |
| 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 528/2404 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| dar 1.7.1 (landing page) Francesc Catala-Moll
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| See other builds for dar in R Universe. | ||||||||||||||
|
To the developers/maintainers of the dar package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/dar.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: dar |
| Version: 1.7.1 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:dar.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings dar_1.7.1.tar.gz |
| StartedAt: 2026-04-23 19:16:03 -0400 (Thu, 23 Apr 2026) |
| EndedAt: 2026-04-23 19:21:02 -0400 (Thu, 23 Apr 2026) |
| EllapsedTime: 299.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: dar.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:dar.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings dar_1.7.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/dar.Rcheck’
* using R version 4.6.0 alpha (2026-04-08 r89818)
* using platform: aarch64-apple-darwin23
* R was compiled by
Apple clang version 17.0.0 (clang-1700.3.19.1)
GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-04-23 23:16:03 UTC
* using option ‘--no-vignettes’
* checking for file ‘dar/DESCRIPTION’ ... OK
* this is package ‘dar’ version ‘1.7.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 21 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 ‘dar’ 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 ... 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 R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
step_maaslin 15.330 0.232 15.704
step_ancom 9.960 0.099 10.126
import_steps 2.952 0.305 25.805
recipe 1.946 0.164 27.235
prep 1.399 0.130 24.331
* 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
dar.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL dar ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’ * installing *source* package ‘dar’ ... ** this is package ‘dar’ version ‘1.7.1’ ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (dar)
dar.Rcheck/tests/testthat.Rout
R version 4.6.0 alpha (2026-04-08 r89818)
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23
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(dar)
>
> test_check("dar")
Starting 2 test processes.
> test-roxytest-tests-recipe-class.R: Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
> test-roxytest-tests-recipe-class.R: Also defined by 'tidytree'
> test-roxytest-tests-recipe-class.R: Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
> test-roxytest-tests-recipe-class.R: Also defined by 'tidytree'
> test-roxytest-tests-recipe-class.R: Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
> test-roxytest-tests-recipe-class.R: Also defined by 'tidytree'
> test-roxytest-tests-recipe-class.R: Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
> test-roxytest-tests-recipe-class.R: Also defined by 'tidytree'
> test-roxytest-tests-recipe-class.R: Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
> test-roxytest-tests-recipe-class.R: Also defined by 'tidytree'
> test-roxytest-tests-recipe-class.R: Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
> test-roxytest-tests-recipe-class.R: Also defined by 'tidytree'
> test-roxytest-tests-recipe-class.R: Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
> test-roxytest-tests-recipe-class.R: Also defined by 'tidytree'
> test-roxytest-tests-recipe-class.R: Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
> test-roxytest-tests-recipe-class.R: Also defined by 'tidytree'
> test-roxytest-tests-recipe-class.R: Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
> test-roxytest-tests-recipe-class.R: Also defined by 'tidytree'
> test-roxytest-tests-recipe-class.R: Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
> test-roxytest-tests-recipe-class.R: Also defined by 'tidytree'
> test-roxytest-tests-recipe-class.R: Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
> test-roxytest-tests-recipe-class.R: Also defined by 'tidytree'
> test-roxytest-tests-recipe-class.R: Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
> test-roxytest-tests-recipe-class.R: Also defined by 'tidytree'
> test-roxytest-tests-recipe-class.R: Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
> test-roxytest-tests-recipe-class.R: Also defined by 'tidytree'
> test-roxytest-tests-recipe-class.R: Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
> test-roxytest-tests-recipe-class.R: Also defined by 'tidytree'
> test-roxytest-tests-recipe-class.R: Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
> test-roxytest-tests-recipe-class.R: Also defined by 'tidytree'
> test-roxytest-tests-recipe-class.R: Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
> test-roxytest-tests-recipe-class.R: Also defined by 'tidytree'
> test-roxytest-tests-recipe-class.R: Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
> test-roxytest-tests-recipe-class.R: Also defined by 'tidytree'
> test-roxytest-tests-recipe-class.R: Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
> test-roxytest-tests-recipe-class.R: Also defined by 'tidytree'
> test-roxytest-tests-recipe-class.R: Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
> test-roxytest-tests-recipe-class.R: Also defined by 'tidytree'
[ FAIL 0 | WARN 3 | SKIP 8 | PASS 110 ]
══ Skipped tests (8) ═══════════════════════════════════════════════════════════
• On CRAN (8): 'test-roxytest-tests-bake.R:5:1',
'test-roxytest-tests-ancom.R:5:1', 'test-roxytest-tests-lefse.R:5:1',
'test-roxytest-tests-maaslin3.R:5:1', 'test-roxytest-tests-pkg_check.R:5:1',
'test-roxytest-tests-misc.R:105:1', 'test-roxytest-tests-misc.R:130:1',
'test-roxytest-tests-steps_and_checks.R:14:1'
[ FAIL 0 | WARN 3 | SKIP 8 | PASS 110 ]
>
> proc.time()
user system elapsed
47.189 2.612 88.397
dar.Rcheck/dar-Ex.timings
| name | user | system | elapsed | |
| abundance_plt | 0.727 | 0.029 | 0.760 | |
| add_step | 1.798 | 0.122 | 1.942 | |
| add_tax | 0.018 | 0.000 | 0.018 | |
| add_var | 0.016 | 0.000 | 0.017 | |
| bake | 0.211 | 0.013 | 0.231 | |
| contains_rarefaction | 0.157 | 0.012 | 0.178 | |
| cool | 0.028 | 0.001 | 0.028 | |
| corr_heatmap | 1.360 | 0.042 | 1.425 | |
| exclusion_plt | 0.385 | 0.011 | 0.406 | |
| find_intersections | 0.049 | 0.000 | 0.049 | |
| get_comparisons | 0.011 | 0.000 | 0.011 | |
| get_phy | 0.015 | 0.001 | 0.015 | |
| get_tax | 0.016 | 0.001 | 0.017 | |
| get_var | 0.017 | 0.001 | 0.017 | |
| import_steps | 2.952 | 0.305 | 25.805 | |
| intersection_df | 0.012 | 0.001 | 0.012 | |
| intersection_plt | 0.485 | 0.004 | 0.491 | |
| mutual_plt | 0.708 | 0.008 | 0.721 | |
| otu_table | 0.125 | 0.002 | 0.130 | |
| overlap_df | 0.021 | 0.001 | 0.022 | |
| phy_qc | 0.612 | 0.022 | 0.638 | |
| prep | 1.399 | 0.130 | 24.331 | |
| rand_id | 0.000 | 0.000 | 0.001 | |
| rarefaction_help | 0.022 | 0.001 | 0.025 | |
| recipe | 1.946 | 0.164 | 27.235 | |
| required_deps | 0.017 | 0.001 | 0.019 | |
| sample_data | 0.018 | 0.001 | 0.019 | |
| step_aldex | 1.581 | 0.380 | 1.994 | |
| step_ancom | 9.960 | 0.099 | 10.126 | |
| step_corncob | 0.515 | 0.025 | 0.544 | |
| step_deseq | 1.742 | 0.012 | 1.760 | |
| step_filter_by_abundance | 0.02 | 0.00 | 0.02 | |
| step_filter_by_prevalence | 0.02 | 0.00 | 0.02 | |
| step_filter_by_rarity | 0.020 | 0.000 | 0.021 | |
| step_filter_by_variance | 0.019 | 0.001 | 0.020 | |
| step_filter_taxa | 0.019 | 0.001 | 0.019 | |
| step_lefse | 0.155 | 0.017 | 0.172 | |
| step_maaslin | 15.330 | 0.232 | 15.704 | |
| step_rarefaction | 0.025 | 0.001 | 0.026 | |
| step_subset_taxa | 0.694 | 0.014 | 1.078 | |
| step_wilcox | 0.044 | 0.005 | 0.049 | |
| steps_ids | 0.008 | 0.001 | 0.009 | |
| tax_table | 0.022 | 0.000 | 0.023 | |
| tidyeval | 0.004 | 0.000 | 0.005 | |
| to_tibble | 0.122 | 0.003 | 0.126 | |
| use_rarefy | 0.008 | 0.000 | 0.008 | |