Back to Multiple platform build/check report for BioC 3.22:   simplified   long
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This page was generated on 2025-10-21 12:07 -0400 (Tue, 21 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" 4642
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 1.5.2  (landing page)
Francesc Catala-Moll
Snapshot Date: 2025-10-20 13:45 -0400 (Mon, 20 Oct 2025)
git_url: https://git.bioconductor.org/packages/dar
git_branch: devel
git_last_commit: 9e7cc12
git_last_commit_date: 2025-10-17 03:32:02 -0400 (Fri, 17 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 taishan

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: dar
Version: 1.5.2
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:dar.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings dar_1.5.2.tar.gz
StartedAt: 2025-10-21 07:09:10 -0000 (Tue, 21 Oct 2025)
EndedAt: 2025-10-21 07:21:31 -0000 (Tue, 21 Oct 2025)
EllapsedTime: 741.4 seconds
RetCode: 0
Status:   OK  
CheckDir: dar.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:dar.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings dar_1.5.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/dar.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘dar/DESCRIPTION’ ... OK
* this is package ‘dar’ version ‘1.5.2’
* 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         20.096  0.947  21.093
step_deseq          8.629  0.212   8.865
prep                6.803  0.620  52.663
corr_heatmap        5.547  0.160   5.724
import_steps        4.717  0.551  46.128
step_metagenomeseq  4.868  0.355  12.840
export_steps        3.121  0.173  17.889
recipe              2.679  0.548  22.014
* 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:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL dar
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘dar’ ...
** this is package ‘dar’ version ‘1.5.2’
** 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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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
[ FAIL 0 | WARN 3 | SKIP 10 | PASS 81 ]

══ Skipped tests (10) ══════════════════════════════════════════════════════════
• On CRAN (9): 'test-roxytest-tests-bake.R:18:3',
  'test-roxytest-tests-lefse.R:15:3', 'test-roxytest-tests-misc.R:73:3',
  'test-roxytest-tests-misc.R:101:3', 'test-roxytest-tests-misc.R:108:3',
  'test-roxytest-tests-pkg_check.R:6:3', 'test-roxytest-tests-maaslin2.R:16:3',
  '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 
266.155  10.335 305.530 

Example timings

dar.Rcheck/dar-Ex.timings

nameusersystemelapsed
abundance_plt4.1700.1834.369
add_tax0.2120.0080.221
add_var0.2180.0040.223
bake0.6290.0120.644
contains_rarefaction0.8180.1280.951
cool0.3850.0000.386
corr_heatmap5.5470.1605.724
exclusion_plt1.5730.0511.630
export_steps 3.121 0.17317.889
find_intersections0.2550.0000.257
get_comparisons0.0230.0000.024
get_phy0.0260.0000.025
get_tax0.0320.0000.031
get_var0.0330.0000.033
import_steps 4.717 0.55146.128
intersection_df0.2220.0080.231
intersection_plt3.4660.2873.766
mutual_plt3.8410.1003.952
otu_table0.6410.0320.674
overlap_df0.3480.0040.353
phy_qc1.7880.0791.874
prep 6.803 0.62052.663
rand_id000
read_data1.8470.3462.208
recipe 2.679 0.54822.014
required_deps0.0410.0000.041
sample_data0.040.000.04
step_aldex20.096 0.94721.093
step_ancom000
step_corncob2.5530.0252.629
step_deseq8.6290.2128.865
step_filter_by_abundance0.0530.0000.052
step_filter_by_prevalence0.0520.0000.052
step_filter_by_rarity0.0480.0040.052
step_filter_by_variance0.0460.0040.050
step_filter_taxa0.0510.0000.051
step_lefse0.0960.0000.097
step_maaslin4.6670.1364.818
step_metagenomeseq 4.868 0.35512.840
step_rarefaction0.0750.0000.076
step_subset_taxa0.0560.0000.057
step_wilcox2.6680.0952.775
steps_ids0.010.000.01
tax_table0.0670.0000.067
tidyeval0.0230.0000.023
to_tibble0.6360.0160.654
use_rarefy0.0170.0000.017
zero_otu0.5950.0000.598