Francesc Catala-Moll
| Snapshot Date: 2026-01-22 13:45 -0500 (Thu, 22 Jan 2026) |
| git_url: https://git.bioconductor.org/packages/dar |
| git_branch: RELEASE_3_22 |
| git_last_commit: 0a164df |
| git_last_commit_date: 2025-10-29 11:27:31 -0500 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-01-26 11:57 -0500 (Mon, 26 Jan 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4886 |
| 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 524/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| dar 1.6.0 (landing page) Francesc Catala-Moll
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
|
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: 1.6.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:dar.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings dar_1.6.0.tar.gz |
| StartedAt: 2026-01-22 22:48:03 -0500 (Thu, 22 Jan 2026) |
| EndedAt: 2026-01-22 23:00:56 -0500 (Thu, 22 Jan 2026) |
| EllapsedTime: 772.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: dar.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:dar.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings dar_1.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/dar.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘dar/DESCRIPTION’ ... OK
* this is package ‘dar’ version ‘1.6.0’
* 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 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 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_aldex 14.103 0.562 14.668
prep 6.014 0.681 40.727
step_deseq 6.090 0.185 6.276
import_steps 4.089 0.225 36.761
step_metagenomeseq 3.226 0.097 9.390
export_steps 2.666 0.205 13.579
recipe 2.381 0.276 17.399
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
dar.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL dar ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘dar’ ... ** this is package ‘dar’ version ‘1.6.0’ ** 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 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-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(dar)
>
> test_check("dar")
Starting 2 test processes.
> test-roxytest-tests-lefse.R: ! Run lefse without rarefaction is not recommended (id = lefse__Croquembouche)
> test-roxytest-tests-recipe-class.R: Loading required namespace: TreeSummarizedExperiment
> 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 10 | PASS 97 ]
══ Skipped tests (10) ══════════════════════════════════════════════════════════
• On CRAN (9): 'test-roxytest-tests-bake.R:5:1',
'test-roxytest-tests-lefse.R:5:1', 'test-roxytest-tests-maaslin2.R:5:1',
'test-roxytest-tests-pkg_check.R:5:1', 'test-roxytest-tests-misc.R:71:1',
'test-roxytest-tests-misc.R:97:1', 'test-roxytest-tests-misc.R:106:1',
'test-roxytest-tests-read_data.R:11:1',
'test-roxytest-tests-steps_and_checks.R:5:1'
• Temporary disabling due to problems with the ANCOM package (1):
'test-roxytest-tests-ancom.R:6:3'
[ FAIL 0 | WARN 3 | SKIP 10 | PASS 97 ]
>
> proc.time()
user system elapsed
139.775 8.202 163.646
dar.Rcheck/dar-Ex.timings
| name | user | system | elapsed | |
| abundance_plt | 2.361 | 0.103 | 2.464 | |
| add_tax | 0.158 | 0.001 | 0.160 | |
| add_var | 0.158 | 0.001 | 0.158 | |
| bake | 0.466 | 0.004 | 0.470 | |
| contains_rarefaction | 0.924 | 0.026 | 0.951 | |
| cool | 0.265 | 0.001 | 0.267 | |
| corr_heatmap | 4.620 | 0.115 | 4.736 | |
| exclusion_plt | 1.026 | 0.002 | 1.028 | |
| export_steps | 2.666 | 0.205 | 13.579 | |
| find_intersections | 0.155 | 0.003 | 0.158 | |
| get_comparisons | 0.020 | 0.000 | 0.021 | |
| get_phy | 0.020 | 0.000 | 0.021 | |
| get_tax | 0.024 | 0.000 | 0.024 | |
| get_var | 0.025 | 0.001 | 0.025 | |
| import_steps | 4.089 | 0.225 | 36.761 | |
| intersection_df | 0.148 | 0.000 | 0.148 | |
| intersection_plt | 2.046 | 0.006 | 2.053 | |
| mutual_plt | 2.338 | 0.038 | 2.376 | |
| otu_table | 0.379 | 0.003 | 0.382 | |
| overlap_df | 0.213 | 0.001 | 0.214 | |
| phy_qc | 1.110 | 0.029 | 1.140 | |
| prep | 6.014 | 0.681 | 40.727 | |
| rand_id | 0 | 0 | 0 | |
| read_data | 1.149 | 0.591 | 1.748 | |
| recipe | 2.381 | 0.276 | 17.399 | |
| required_deps | 0.034 | 0.003 | 0.038 | |
| sample_data | 0.032 | 0.000 | 0.033 | |
| step_aldex | 14.103 | 0.562 | 14.668 | |
| step_ancom | 0 | 0 | 0 | |
| step_corncob | 2.033 | 0.025 | 2.059 | |
| step_deseq | 6.090 | 0.185 | 6.276 | |
| step_filter_by_abundance | 0.037 | 0.002 | 0.039 | |
| step_filter_by_prevalence | 0.039 | 0.000 | 0.039 | |
| step_filter_by_rarity | 0.041 | 0.001 | 0.042 | |
| step_filter_by_variance | 0.037 | 0.002 | 0.039 | |
| step_filter_taxa | 0.036 | 0.001 | 0.037 | |
| step_lefse | 0.064 | 0.002 | 0.067 | |
| step_maaslin | 3.060 | 0.095 | 3.156 | |
| step_metagenomeseq | 3.226 | 0.097 | 9.390 | |
| step_rarefaction | 0.156 | 0.051 | 0.207 | |
| step_subset_taxa | 0.036 | 0.003 | 0.039 | |
| step_wilcox | 1.651 | 0.107 | 1.758 | |
| steps_ids | 0.009 | 0.001 | 0.011 | |
| tax_table | 0.042 | 0.010 | 0.052 | |
| tidyeval | 0.013 | 0.003 | 0.017 | |
| to_tibble | 0.419 | 0.012 | 0.431 | |
| use_rarefy | 0.014 | 0.001 | 0.016 | |
| zero_otu | 0.394 | 0.023 | 0.418 | |