Back to Multiple platform build/check report for BioC 3.22:   simplified   long
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This page was generated on 2025-09-20 12:03 -0400 (Sat, 20 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4814
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4603
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4547
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4553
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 517/2333HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dar 1.5.0  (landing page)
Francesc Catala-Moll
Snapshot Date: 2025-09-19 13:45 -0400 (Fri, 19 Sep 2025)
git_url: https://git.bioconductor.org/packages/dar
git_branch: devel
git_last_commit: 54aa2bf
git_last_commit_date: 2025-04-15 13:27:21 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 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  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for dar on nebbiolo2

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: 1.5.0
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:dar.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings dar_1.5.0.tar.gz
StartedAt: 2025-09-19 22:55:39 -0400 (Fri, 19 Sep 2025)
EndedAt: 2025-09-19 23:16:34 -0400 (Fri, 19 Sep 2025)
EllapsedTime: 1254.8 seconds
RetCode: 0
Status:   OK  
CheckDir: dar.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:dar.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings dar_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/dar.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘dar/DESCRIPTION’ ... OK
* this is package ‘dar’ version ‘1.5.0’
* 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 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         19.443  1.001  21.630
prep                8.019  0.704  63.598
step_deseq          8.442  0.232  11.985
corr_heatmap        5.852  0.295   7.203
import_steps        5.259  0.483  52.187
step_metagenomeseq  4.428  0.071  14.253
export_steps        3.539  0.366  21.072
recipe              2.935  0.293  27.207
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

dar.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL dar
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘dar’ ...
** this is package ‘dar’ version ‘1.5.0’
** 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 (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-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-maaslin2.R:16:3',
  '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 
258.445  11.635 375.968 

Example timings

dar.Rcheck/dar-Ex.timings

nameusersystemelapsed
abundance_plt3.4520.1473.711
add_tax0.1930.0110.203
add_var0.2060.0040.243
bake0.6990.0040.703
contains_rarefaction0.9850.0881.074
cool0.4280.0040.432
corr_heatmap5.8520.2957.203
exclusion_plt1.5970.0452.015
export_steps 3.539 0.36621.072
find_intersections0.2330.0220.296
get_comparisons0.0340.0010.035
get_phy0.0250.0030.028
get_tax0.0340.0000.034
get_var0.0330.0010.034
import_steps 5.259 0.48352.187
intersection_df0.2610.0030.264
intersection_plt2.7720.1233.041
mutual_plt3.2090.1353.919
otu_table0.5350.0020.658
overlap_df0.3210.0030.380
phy_qc1.3960.0263.274
prep 8.019 0.70463.598
rand_id000
read_data2.2930.7144.509
recipe 2.935 0.29327.207
required_deps0.0730.0040.077
sample_data0.0480.0010.049
step_aldex19.443 1.00121.630
step_ancom0.0010.0000.000
step_corncob2.6030.0314.226
step_deseq 8.442 0.23211.985
step_filter_by_abundance0.0630.0000.063
step_filter_by_prevalence0.0620.0010.063
step_filter_by_rarity0.0620.0000.062
step_filter_by_variance0.060.000.06
step_filter_taxa0.0610.0000.068
step_lefse0.0950.0010.113
step_maaslin4.6190.1154.859
step_metagenomeseq 4.428 0.07114.253
step_rarefaction0.0500.0020.052
step_subset_taxa0.0400.0020.041
step_wilcox1.7720.7432.517
steps_ids0.0150.0030.018
tax_table0.0470.0070.054
tidyeval0.0130.0040.017
to_tibble0.4270.1710.599
use_rarefy0.0140.0000.015
zero_otu0.3950.0630.457