##############################################################################
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###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:dar.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings dar_1.3.0.tar.gz
###
##############################################################################
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* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/dar.Rcheck'
* using R Under development (unstable) (2025-01-21 r87610 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 ... OK
* 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 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)
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   20.34   2.97   23.32
corr_heatmap  4.03   0.19    6.35
prep          2.45   0.20   43.70
export_steps  1.50   0.20   16.79
import_steps  1.43   0.16   43.27
recipe        0.75   0.07   19.05
* 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
  'E:/biocbuild/bbs-3.21-bioc/meat/dar.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL dar
###
##############################################################################
##############################################################################


* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'dar' ...
** this is package 'dar' version '1.3.0'
** 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)

R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 0 | SKIP 9 | PASS 81 ]

══ Skipped tests (9) ═══════════════════════════════════════════════════════════
• 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'

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-roxytest-tests-ancom.R:14:3'): [unknown alias] @ L113 ──────────
<purrr_error_indexed/rlang_error/error/condition>
Error in `(function (.x, .f, ..., .progress = FALSE) 
{
    map_("list", .x, .f, ..., .progress = .progress)
})(.x = "rec %>% run_ancom(fix_formula = c('RiskGroup2'), rand_formula = NULL, p_adj_method = c('holm'), prv_cut = 0.1, lib_cut = 0, s0_perc = 0.05, group = NULL, struc_zero = FALSE, neg_lb = FALSE, alpha = 0.05, n_cl = 1, verbose = FALSE, global = FALSE, pairwise = FALSE, dunnet = FALSE, trend = FALSE, rarefy = FALSE)", 
    .f = function (...) 
    {
        {
            ...furrr_chunk_seeds_i <- ...furrr_chunk_seeds_env[["i"]]
            ...furrr_chunk_seeds_env[["i"]] <- ...furrr_chunk_seeds_i + 
                1L
            assign(x = ".Random.seed", value = ...furrr_chunk_seeds[[...furrr_chunk_seeds_i]], 
                envir = globalenv(), inherits = FALSE)
        }
        NULL
        ...furrr_out <- ...furrr_fn(...)
        ...furrr_out
    })`: 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$max_iter)
    }
  }`:
! task 1 failed - "values must be length 1,
 but FUN(X[[2]]) result is length 0"
Backtrace:
     ▆
  1. ├─parallel (local) workRSOCK()
  2. │ └─parallel:::workLoop(...)
  3. │   └─parallel:::workCommand(master)
  4. │     ├─base::tryCatch(...)
  5. │     │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  6. │     │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
  7. │     │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
  8. │     ├─base::tryCatch(...)
  9. │     │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 10. │     │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 11. │     │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 12. │     ├─base::do.call(msg$data$fun, msg$data$args, quote = TRUE)
 13. │     └─future (local) `<fn>`(...)
 14. │       └─base::eval(expr, envir = envir, enclos = enclos)
 15. │         └─base::eval(expr, envir = envir, enclos = enclos)
 16. ├─base::tryCatch(...)
 17. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 18. │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 19. │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 20. ├─base::withCallingHandlers(...)
 21. ├─base::withVisible(...)
 22. ├─base::local(...)
 23. │ └─base::eval.parent(substitute(eval(quote(expr), envir)))
 24. │   └─base::eval(expr, p)
 25. │     └─base::eval(expr, p)
 26. ├─base::eval(...)
 27. │ └─base::eval(...)
 28. │   ├─base::withCallingHandlers(...)
 29. │   ├─base::do.call(...furrr_map_fn, args)
 30. │   └─purrr (local) `<fn>`(...)
 31. │     └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
 32. │       ├─purrr:::with_indexed_errors(...)
 33. │       │ └─base::withCallingHandlers(...)
 34. │       ├─purrr:::call_with_cleanup(...)
 35. │       └─.f(.x[[i]], ...)
 36. │         └─dar (local) ...furrr_fn(...)
 37. │           ├─base::eval(parse(text = .x))
 38. │           │ └─base::eval(parse(text = .x))
 39. │           └─rec %>% ...
 40. ├─dar:::run_ancom(...)
 41. │ └─vars %>% purrr::set_names() %>% ...
 42. ├─purrr::map(...)
 43. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
 44. │   ├─purrr:::with_indexed_errors(...)
 45. │   │ └─base::withCallingHandlers(...)
 46. │   ├─purrr:::call_with_cleanup(...)
 47. │   └─dar (local) .f(.x[[i]], ...)
 48. │     └─get_comparisons(var, phy, as_list = TRUE, n_cut = 1) %>% ...
 49. ├─purrr::map_dfr(...)
 50. │ └─purrr::map(.x, .f, ...)
 51. │   └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
 52. │     ├─purrr:::with_indexed_errors(...)
 53. │     │ └─base::withCallingHandlers(...)
 54. │     ├─purrr:::call_with_cleanup(...)
 55. │     └─dar (local) .f(.x[[i]], ...)
 56. │       └─ANCOMBC::ancombc2(...)
 57. │         ├─... %dorng% ...
 58. │         │ └─base::do.call(`%dopar%`, list(obj, ex), envir = parent.frame())
 59. │         └─foreach (local) `<fn>`(...)
 60. │           └─e$fun(obj, substitute(ex), parent.frame(), e$data)
 61. │             └─base::stop(simpleError(msg, call = expr))
 62. ├─purrr (local) `<fn>`(`<smplErrr>`)
 63. │ └─cli::cli_abort(...)
 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