##############################################################################
##############################################################################
###
### 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_1.3.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/dar.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘dar/DESCRIPTION’ ... OK
* this is package ‘dar’ version ‘1.3.0’
* 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 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 ... ERROR
Running examples in ‘dar-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: step_ancom
> ### Title: ANCOM analysis
> ### Aliases: step_ancom step_ancom,Recipe-method
> ###   step_ancom,PrepRecipe-method
> 
> ### ** Examples
> 
> data(metaHIV_phy)
> 
> ## Init Recipe
> rec <-
+   recipe(metaHIV_phy, "RiskGroup2", "Phylum") |>
+   step_subset_taxa(tax_level = "Kingdom", taxa = c("Bacteria", "Archaea")) |>
+   step_filter_taxa(.f = "function(x) sum(x > 0) >= (0.4 * length(x))")
> 
> rec
── DAR Recipe ──────────────────────────────────────────────────────────────────
Inputs:

     ℹ phyloseq object with 451 taxa and 156 samples 
     ℹ variable of interes RiskGroup2 (class: character, levels: hts, msm, pwid) 
     ℹ taxonomic level Phylum 

Preporcessing steps:

     ◉ step_subset_taxa() id = subset_taxa__Fa_gao 
     ◉ step_filter_taxa() id = filter_taxa__Pogača 

DA steps:

> 
> ## Define step with default parameters and prep
> rec <-
+   step_ancom(rec) |>
+   prep(parallel = FALSE)
2025-02-09 18:52:25.024 R[10642:477548854] XType: Using static font registry.
Warning: The number of taxa used for estimating sample-specific biases is: 6
A large number of taxa (>50) is required for the consistent estimation of biases
Warning in data.frame(y_crt = unlist(y[i, ]) - theta, meta_data) :
  row names were found from a short variable and have been discarded
Warning in data.frame(y_crt = unlist(y[i, ]) - theta, meta_data) :
  row names were found from a short variable and have been discarded
Warning in data.frame(y_crt = unlist(y[i, ]) - theta, meta_data) :
  row names were found from a short variable and have been discarded
Warning in data.frame(y_crt = unlist(y[i, ]) - theta, meta_data) :
  row names were found from a short variable and have been discarded
Warning in data.frame(y_crt = unlist(y[i, ]) - theta, meta_data) :
  row names were found from a short variable and have been discarded
Warning in data.frame(y_crt = unlist(y[i, ]) - theta, meta_data) :
  row names were found from a short variable and have been discarded
Warning in data.frame(y_crt = unlist(y[i, ]) - theta, meta_data) :
  row names were found from a short variable and have been discarded
Warning in data.frame(y_crt = unlist(y[i, ]) - theta, meta_data) :
  row names were found from a short variable and have been discarded
Warning in data.frame(y_crt = unlist(y[i, ]) - theta, meta_data) :
  row names were found from a short variable and have been discarded
Warning in data.frame(y_crt = unlist(y[i, ]) - theta, meta_data) :
  row names were found from a short variable and have been discarded
Warning in data.frame(y_crt = unlist(y[i, ]) - theta, meta_data) :
  row names were found from a short variable and have been discarded
Warning in data.frame(y_crt = unlist(y[i, ]) - theta, meta_data) :
  row names were found from a short variable and have been discarded
Loading required package: foreach
Loading required package: rngtools
Warning in min(beta, na.rm = TRUE) :
  no non-missing arguments to min; returning Inf
Warning in max(beta, na.rm = TRUE) :
  no non-missing arguments to max; returning -Inf
Warning in min(beta, na.rm = TRUE) :
  no non-missing arguments to min; returning Inf
Warning in max(beta, na.rm = TRUE) :
  no non-missing arguments to max; returning -Inf
Error in `purrr::map()`:
ℹ In index: 1.
Caused by error in `purrr::map()`:
ℹ In index: 1.
ℹ With name: RiskGroup2.
Caused by error in `map()`:
ℹ In index: 1.
Caused by error in `{
    {
      rngtools::RNGseed(.doRNG.stream)
    }
    {
      output = fun_list[[1]](beta = beta1[, i], var_hat = var_hat1[, i], tol = em_control$
        tol, max_iter = em_control$max_iter)
    }
  }`:
! task 1 failed - "values must be length 1,
 but FUN(X[[2]]) result is length 0"
Backtrace:
     ▆
  1. ├─dar::prep(step_ancom(rec), parallel = FALSE)
  2. ├─dar::prep(step_ancom(rec), parallel = FALSE)
  3. │ └─... %>% ...
  4. ├─purrr::map(...)
  5. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
  6. │   ├─purrr:::with_indexed_errors(...)
  7. │   │ └─base::withCallingHandlers(...)
  8. │   ├─purrr:::call_with_cleanup(...)
  9. │   └─dar (local) .f(.x[[i]], ...)
 10. │     ├─base::eval(parse(text = .x))
 11. │     │ └─base::eval(parse(text = .x))
 12. │     └─rec %>% ...
 13. ├─dar:::run_ancom(...)
 14. │ └─vars %>% purrr::set_names() %>% ...
 15. ├─purrr::map(...)
 16. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
 17. │   ├─purrr:::with_indexed_errors(...)
 18. │   │ └─base::withCallingHandlers(...)
 19. │   ├─purrr:::call_with_cleanup(...)
 20. │   └─dar (local) .f(.x[[i]], ...)
 21. │     └─get_comparisons(var, phy, as_list = TRUE, n_cut = 1) %>% ...
 22. ├─purrr::map_dfr(...)
 23. │ └─purrr::map(.x, .f, ...)
 24. │   └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
 25. │     ├─purrr:::with_indexed_errors(...)
 26. │     │ └─base::withCallingHandlers(...)
 27. │     ├─purrr:::call_with_cleanup(...)
 28. │     └─dar (local) .f(.x[[i]], ...)
 29. │       └─ANCOMBC::ancombc2(...)
 30. │         ├─... %dorng% ...
 31. │         │ └─base::do.call(`%dopar%`, list(obj, ex), envir = parent.frame())
 32. │         └─foreach (local) `<fn>`(...)
 33. │           └─e$fun(obj, substitute(ex), parent.frame(), e$data)
 34. │             └─base::stop(simpleError(msg, call = expr))
 35. └─purrr (local) `<fn>`(`<smplErrr>`)
 36.   └─cli::cli_abort(...)
 37.     └─rlang::abort(...)
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
step_aldex   6.482  0.803   7.292
prep         0.643  0.026  12.197
import_steps 0.505  0.029  12.335
recipe       0.243  0.009   6.037
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   64. │   └─rlang::abort(...)
   65. │     └─rlang:::signal_abort(cnd, .file)
   66. │       └─base::signalCondition(cnd)
   67. ├─purrr (local) `<fn>`(`<prrr_rr_>`)
   68. │ └─cli::cli_abort(...)
   69. │   └─rlang::abort(...)
   70. │     └─rlang:::signal_abort(cnd, .file)
   71. │       └─base::signalCondition(cnd)
   72. └─purrr (local) `<fn>`(`<prrr_rr_>`)
   73.   └─cli::cli_abort(...)
   74.     └─rlang::abort(...)
  
  [ FAIL 1 | WARN 0 | SKIP 9 | PASS 81 ]
  Error: Test failures
  Execution halted
* 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: 2 ERRORs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/dar.Rcheck/00check.log’
for details.