Back to Multiple platform build/check report for BioC 3.22:   simplified   long
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This page was generated on 2025-10-17 12:07 -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 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: 1.5.1
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_1.5.1.tar.gz
StartedAt: 2025-10-17 07:54:55 -0000 (Fri, 17 Oct 2025)
EndedAt: 2025-10-17 08:07:04 -0000 (Fri, 17 Oct 2025)
EllapsedTime: 728.4 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_1.5.1.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 ‘1.5.1’
* 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 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         20.203  0.486  20.758
step_deseq          8.642  0.089   8.764
prep                6.686  0.683  51.969
corr_heatmap        5.353  0.135   5.508
import_steps        4.509  0.367  45.217
step_metagenomeseq  4.676  0.021  12.385
export_steps        2.950  0.250  16.873
recipe              2.693  0.186  22.118
* 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 ‘1.5.1’
** 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 4.5.0 (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 
264.498  12.840 304.110 

dar.Rcheck/tests/testthat.Rout.fail


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 1 | WARN 3 | SKIP 10 | PASS 80 ]

══ 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'

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-roxytest-tests-recipe-class.R:15:3'): Function recipe() @ L124 ──
Error in `.requirePackage(package)`: unable to load required package 'GenomeInfoDb'
Backtrace:
     ▆
  1. ├─testthat::expect_s4_class(recipe(GlobalPatterns), "Recipe") at test-roxytest-tests-recipe-class.R:15:3
  2. │ └─testthat::quasi_label(enquo(object), arg = "object")
  3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
  4. ├─dar::recipe(GlobalPatterns)
  5. │ ├─mia::convertToPhyloseq(microbiome_object)
  6. │ └─mia::convertToPhyloseq(microbiome_object)
  7. │   └─mia (local) .local(x, ...)
  8. │     ├─x[rowLinks(x)$whichTree == tree.name, ]
  9. │     └─x[rowLinks(x)$whichTree == tree.name, ]
 10. │       ├─BiocGenerics::updateObject(x)
 11. │       └─TreeSummarizedExperiment::updateObject(x)
 12. │         ├─methods::callNextMethod()
 13. │         └─SingleCellExperiment (local) .nextMethod(object = object)
 14. │           ├─methods::callNextMethod()
 15. │           └─SummarizedExperiment (local) .nextMethod(object = object)
 16. │             ├─BiocGenerics::updateObject(object@rowRanges, ..., verbose = verbose)
 17. │             └─GenomicRanges::updateObject(object@rowRanges, ..., verbose = verbose)
 18. │               ├─BiocGenerics::updateObject(object@unlistData, ..., verbose = verbose)
 19. │               └─GenomicRanges::updateObject(object@unlistData, ..., verbose = verbose)
 20. │                 └─BiocGenerics::updateObject(object@seqinfo, ..., verbose = verbose)
 21. └─methods:::.extendsForS3(`<chr>`)
 22.   └─methods::extends(Class, maybe = FALSE)
 23.     └─methods::getClassDef(class1)
 24.       └─methods:::.requirePackage(package)

[ FAIL 1 | WARN 3 | SKIP 10 | PASS 80 ]
Error: Test failures
Execution halted

Example timings

dar.Rcheck/dar-Ex.timings

nameusersystemelapsed
abundance_plt3.7490.1003.864
add_tax0.2120.0000.213
add_var0.2160.0000.217
bake0.6120.0000.613
contains_rarefaction0.7920.0520.849
cool0.3710.0040.377
corr_heatmap5.3530.1355.508
exclusion_plt1.5020.0201.527
export_steps 2.950 0.25016.873
find_intersections0.2170.0200.236
get_comparisons0.0230.0000.023
get_phy0.0250.0000.025
get_tax0.0250.0040.029
get_var0.030.000.03
import_steps 4.509 0.36745.217
intersection_df0.2170.0000.218
intersection_plt3.2160.1473.374
mutual_plt3.6750.1523.840
otu_table0.5980.0040.605
overlap_df0.3290.0040.334
phy_qc1.6890.0401.734
prep 6.686 0.68351.969
rand_id000
read_data1.7480.3752.143
recipe 2.693 0.18622.118
required_deps0.0390.0030.043
sample_data0.0360.0040.040
step_aldex20.203 0.48620.758
step_ancom0.0000.0000.001
step_corncob2.6230.0312.677
step_deseq8.6420.0898.764
step_filter_by_abundance0.050.000.05
step_filter_by_prevalence0.0490.0000.049
step_filter_by_rarity0.0480.0000.048
step_filter_by_variance0.050.000.05
step_filter_taxa0.0450.0040.049
step_lefse0.0860.0000.086
step_maaslin4.3690.0564.444
step_metagenomeseq 4.676 0.02112.385
step_rarefaction0.0610.0000.061
step_subset_taxa0.0490.0000.049
step_wilcox2.4710.0042.485
steps_ids0.010.000.01
tax_table0.0620.0000.062
tidyeval0.0180.0040.021
to_tibble0.6290.0000.631
use_rarefy0.0160.0000.015
zero_otu0.5880.0000.591