Francesc Catala-Moll
| Snapshot Date: 2025-11-16 13:40 -0500 (Sun, 16 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/dar |
| git_branch: devel |
| git_last_commit: 6a93481 |
| git_last_commit_date: 2025-10-29 11:27:31 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-17 11:39 -0500 (Mon, 17 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4826 |
| lconway | macOS 12.7.6 Monterey | x86_64 | R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences" | 4491 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4562 |
| 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 514/2325 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| dar 1.7.0 (landing page) Francesc Catala-Moll
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | 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: 1.7.0 |
| 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_1.7.0.tar.gz |
| StartedAt: 2025-11-17 02:14:29 -0500 (Mon, 17 Nov 2025) |
| EndedAt: 2025-11-17 02:23:57 -0500 (Mon, 17 Nov 2025) |
| EllapsedTime: 567.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: dar.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### 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_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/dar.Rcheck’
* using R Under development (unstable) (2025-10-21 r88958)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘dar/DESCRIPTION’ ... OK
* this is package ‘dar’ version ‘1.7.0’
* 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 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 17.727 3.223 22.388
step_deseq 6.493 0.260 6.842
corr_heatmap 4.981 0.172 5.164
prep 4.617 0.116 42.327
import_steps 3.913 0.156 39.328
step_metagenomeseq 3.232 0.071 10.490
export_steps 2.911 0.243 15.432
recipe 2.316 0.062 19.343
* 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-x86_64/Resources/library’ * installing *source* package ‘dar’ ... ** this is package ‘dar’ version ‘1.7.0’ ** 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 Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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__Conejito)
> 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
150.301 11.097 191.560
dar.Rcheck/dar-Ex.timings
| name | user | system | elapsed | |
| abundance_plt | 2.631 | 0.075 | 2.713 | |
| add_tax | 0.177 | 0.006 | 0.183 | |
| add_var | 0.190 | 0.006 | 0.196 | |
| bake | 0.533 | 0.011 | 0.546 | |
| contains_rarefaction | 0.888 | 0.020 | 0.913 | |
| cool | 0.316 | 0.005 | 0.321 | |
| corr_heatmap | 4.981 | 0.172 | 5.164 | |
| exclusion_plt | 1.181 | 0.010 | 1.193 | |
| export_steps | 2.911 | 0.243 | 15.432 | |
| find_intersections | 0.154 | 0.003 | 0.157 | |
| get_comparisons | 0.016 | 0.002 | 0.018 | |
| get_phy | 0.023 | 0.003 | 0.025 | |
| get_tax | 0.030 | 0.002 | 0.032 | |
| get_var | 0.032 | 0.002 | 0.034 | |
| import_steps | 3.913 | 0.156 | 39.328 | |
| intersection_df | 0.157 | 0.004 | 0.161 | |
| intersection_plt | 2.275 | 0.032 | 2.312 | |
| mutual_plt | 2.452 | 0.013 | 2.472 | |
| otu_table | 0.376 | 0.004 | 0.381 | |
| overlap_df | 0.249 | 0.005 | 0.254 | |
| phy_qc | 1.174 | 0.021 | 1.196 | |
| prep | 4.617 | 0.116 | 42.327 | |
| rand_id | 0 | 0 | 0 | |
| read_data | 1.453 | 0.365 | 1.564 | |
| recipe | 2.316 | 0.062 | 19.343 | |
| required_deps | 0.039 | 0.007 | 0.047 | |
| sample_data | 0.030 | 0.003 | 0.033 | |
| step_aldex | 17.727 | 3.223 | 22.388 | |
| step_ancom | 0.000 | 0.000 | 0.001 | |
| step_corncob | 2.020 | 0.156 | 2.197 | |
| step_deseq | 6.493 | 0.260 | 6.842 | |
| step_filter_by_abundance | 0.047 | 0.006 | 0.053 | |
| step_filter_by_prevalence | 0.042 | 0.004 | 0.047 | |
| step_filter_by_rarity | 0.045 | 0.007 | 0.053 | |
| step_filter_by_variance | 0.043 | 0.004 | 0.047 | |
| step_filter_taxa | 0.035 | 0.004 | 0.038 | |
| step_lefse | 0.056 | 0.004 | 0.060 | |
| step_maaslin | 3.253 | 0.182 | 3.445 | |
| step_metagenomeseq | 3.232 | 0.071 | 10.490 | |
| step_rarefaction | 0.058 | 0.007 | 0.065 | |
| step_subset_taxa | 0.048 | 0.006 | 0.054 | |
| step_wilcox | 1.937 | 0.072 | 2.015 | |
| steps_ids | 0.010 | 0.003 | 0.013 | |
| tax_table | 0.053 | 0.004 | 0.058 | |
| tidyeval | 0.018 | 0.001 | 0.018 | |
| to_tibble | 0.345 | 0.004 | 0.348 | |
| use_rarefy | 0.017 | 0.005 | 0.023 | |
| zero_otu | 0.401 | 0.010 | 0.412 | |