Back to Multiple platform build/check report for BioC 3.21:   simplified   long
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This page was generated on 2025-10-13 11:40 -0400 (Mon, 13 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4833
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4614
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4555
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4586
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 516/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dar 1.4.0  (landing page)
Francesc Catala-Moll
Snapshot Date: 2025-10-09 13:40 -0400 (Thu, 09 Oct 2025)
git_url: https://git.bioconductor.org/packages/dar
git_branch: RELEASE_3_21
git_last_commit: 3100bff
git_last_commit_date: 2025-04-15 13:27:21 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    ERROR  skipped


CHECK results for dar on kjohnson1

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.

raw results


Summary

Package: dar
Version: 1.4.0
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_1.4.0.tar.gz
StartedAt: 2025-10-10 19:30:09 -0400 (Fri, 10 Oct 2025)
EndedAt: 2025-10-10 19:45:29 -0400 (Fri, 10 Oct 2025)
EllapsedTime: 920.2 seconds
RetCode: 0
Status:   OK  
CheckDir: dar.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/dar.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘dar/DESCRIPTION’ ... OK
* this is package ‘dar’ version ‘1.4.0’
* 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         19.777  2.430  26.812
step_deseq          7.224  0.244   8.404
corr_heatmap        5.620  0.181   7.352
prep                4.820  0.316  60.690
step_metagenomeseq  3.564  0.102  12.254
export_steps        2.779  0.200  20.184
import_steps        2.664  0.126  52.993
recipe              1.858  0.048  27.274
* 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

dar.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL dar
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘dar’ ...
** this is package ‘dar’ version ‘1.4.0’
** 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)

Tests output

dar.Rcheck/tests/testthat.Rout


R version 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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
[ FAIL 0 | WARN 3 | SKIP 10 | PASS 81 ]

══ Skipped tests (10) ══════════════════════════════════════════════════════════
• On CRAN (9): 'test-roxytest-tests-bake.R:18:3',
  'test-roxytest-tests-maaslin2.R:16:3', 'test-roxytest-tests-lefse.R:15:3',
  'test-roxytest-tests-pkg_check.R:6:3', 'test-roxytest-tests-misc.R:73:3',
  'test-roxytest-tests-misc.R:101:3', 'test-roxytest-tests-misc.R:108:3',
  'test-roxytest-tests-read_data.R:24:3',
  'test-roxytest-tests-steps_and_checks.R:7:3'
• Temporary disabling due to problems with the ANCOM package (1):
  'test-roxytest-tests-ancom.R:6:3'

[ FAIL 0 | WARN 3 | SKIP 10 | PASS 81 ]
> 
> proc.time()
   user  system elapsed 
261.111  21.468 436.609 

Example timings

dar.Rcheck/dar-Ex.timings

nameusersystemelapsed
abundance_plt3.2830.1024.344
add_tax0.2010.0090.274
add_var0.2030.0100.258
bake0.5570.0170.725
contains_rarefaction1.0970.0271.442
cool0.3340.0090.423
corr_heatmap5.6200.1817.352
exclusion_plt1.2920.0301.644
export_steps 2.779 0.20020.184
find_intersections0.2020.0050.250
get_comparisons0.0340.0030.052
get_phy0.0270.0030.039
get_tax0.0350.0040.059
get_var0.0300.0030.038
import_steps 2.664 0.12652.993
intersection_df0.2060.0080.265
intersection_plt2.4880.0333.132
mutual_plt2.7990.0343.569
otu_table0.4350.0070.560
overlap_df0.3050.0100.408
phy_qc1.3310.0381.725
prep 4.820 0.31660.690
rand_id000
read_data1.4820.1542.055
recipe 1.858 0.04827.274
required_deps0.0660.0090.084
sample_data0.0430.0030.063
step_aldex19.777 2.43026.812
step_ancom0.0000.0000.001
step_corncob2.3370.1642.834
step_deseq7.2240.2448.404
step_filter_by_abundance0.0460.0050.059
step_filter_by_prevalence0.0490.0050.055
step_filter_by_rarity0.0480.0070.065
step_filter_by_variance0.0500.0100.064
step_filter_taxa0.0490.0110.062
step_lefse0.0760.0080.087
step_maaslin3.4280.2643.962
step_metagenomeseq 3.564 0.10212.254
step_rarefaction0.0630.0090.077
step_subset_taxa0.0510.0070.069
step_wilcox1.9970.0392.173
steps_ids0.0110.0040.016
tax_table0.0540.0030.061
tidyeval0.0170.0020.020
to_tibble0.3090.0200.373
use_rarefy0.0080.0070.017
zero_otu0.4090.0180.456