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###
### 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
###
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* 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

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL dar
###
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* 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)

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 

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