Back to Multiple platform build/check report for BioC 3.22:   simplified   long
ABC[D]EFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2025-10-17 12:06 -0400 (Fri, 17 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4887
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4677
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4622
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4632
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 521/2353HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dar 1.5.1  (landing page)
Francesc Catala-Moll
Snapshot Date: 2025-10-16 13:45 -0400 (Thu, 16 Oct 2025)
git_url: https://git.bioconductor.org/packages/dar
git_branch: devel
git_last_commit: 0dad027
git_last_commit_date: 2025-10-14 14:50:27 -0400 (Tue, 14 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  NO, package depends on 'mia' which is only available as a source package that needs compilation
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  NO, package depends on 'mia' which is only available as a source package that needs compilation
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for dar on kjohnson3

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: 1.5.1
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_1.5.1.tar.gz
StartedAt: 2025-10-16 19:19:48 -0400 (Thu, 16 Oct 2025)
EndedAt: 2025-10-16 19:23:56 -0400 (Thu, 16 Oct 2025)
EllapsedTime: 248.0 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_1.5.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/dar.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* 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 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘dar/DESCRIPTION’ ... OK
* this is package ‘dar’ version ‘1.5.1’
* 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_aldex   6.362  0.791   7.171
prep         1.528  0.042  13.941
import_steps 0.778  0.035  12.269
recipe       0.557  0.011   6.339
* 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 ‘1.5.1’
** 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)

Tests output

dar.Rcheck/tests/testthat.Rout


R version 4.5.1 Patched (2025-09-10 r88807) -- "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 
 86.013   6.576 123.745 

Example timings

dar.Rcheck/dar-Ex.timings

nameusersystemelapsed
abundance_plt0.9400.0170.961
add_tax0.0520.0010.054
add_var0.0540.0020.056
bake0.1410.0020.144
contains_rarefaction0.3530.0050.363
cool0.0840.0020.087
corr_heatmap1.7420.0611.807
exclusion_plt0.3440.0120.356
export_steps0.8680.0624.840
find_intersections0.0500.0010.051
get_comparisons0.0080.0000.008
get_phy0.0080.0010.009
get_tax0.0100.0010.011
get_var0.0100.0010.011
import_steps 0.778 0.03512.269
intersection_df0.0490.0020.055
intersection_plt0.6640.0040.673
mutual_plt0.7230.0060.728
otu_table0.1180.0020.120
overlap_df0.0710.0010.072
phy_qc0.3320.0080.341
prep 1.528 0.04213.941
rand_id0.0000.0000.001
read_data0.4490.1800.513
recipe0.5570.0116.339
required_deps0.0130.0020.015
sample_data0.0130.0010.014
step_aldex6.3620.7917.171
step_ancom000
step_corncob0.6100.0630.672
step_deseq1.8540.0441.904
step_filter_by_abundance0.0150.0020.017
step_filter_by_prevalence0.0150.0020.016
step_filter_by_rarity0.0140.0020.016
step_filter_by_variance0.0140.0020.017
step_filter_taxa0.0140.0020.016
step_lefse0.0210.0030.024
step_maaslin0.9280.0550.990
step_metagenomeseq0.9750.0253.286
step_rarefaction0.0170.0020.019
step_subset_taxa0.0150.0020.016
step_wilcox0.5060.0110.517
steps_ids0.0050.0010.005
tax_table0.0170.0030.019
tidyeval0.0050.0010.005
to_tibble0.1110.0010.112
use_rarefy0.0080.0040.012
zero_otu0.1180.0030.121