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###
### 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_1.1.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/dar.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘dar/DESCRIPTION’ ... OK
* this is package ‘dar’ version ‘1.1.0’
* 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 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
step_aldex         7.847  0.982  11.006
step_ancom         6.512  0.294   8.625
step_metagenomeseq 1.481  0.040   5.226
prep               0.889  0.043  20.230
export_steps       0.819  0.095   7.045
import_steps       0.725  0.052  19.371
recipe             0.363  0.016   9.801
* 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:
  i In index: 1.
  i With name: RiskGroup2.
  Caused by error in `map()`:
  i In index: 1.
  Caused by error in `dplyr::rename()`:
  ! Can't rename columns that don't exist.
  x Column `Names` doesn't exist.
  Backtrace:
      ▆
   1. └─testthat::expect_snapshot(...) at test-roxytest-tests-lefse.R:15:3
   2.   └─rlang::cnd_signal(state$error)
  
  [ 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: 1 ERROR
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/dar.Rcheck/00check.log’
for details.

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###
### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL dar
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘dar’ ...
** 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 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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-ancom.R:14:3', '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'

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-roxytest-tests-lefse.R:15:3'): [unknown alias] @ L82 ───────────
<purrr_error_indexed/rlang_error/error/condition>
Error in `(function (.x, .f, ..., .progress = FALSE) 
{
    map_("list", .x, .f, ..., .progress = .progress)
})(.x = "rec %>% run_lefse(kruskal.threshold = 0.05, wilcox.threshold = 0.05, lda.threshold = 2, blockCol = NULL, assay = 1, trim.names = FALSE, rarefy = TRUE)", 
    .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 `dplyr::rename()`:
! Can't rename columns that don't exist.
x Column `Names` doesn't exist.
Backtrace:
    ▆
 1. └─testthat::expect_snapshot(...) at test-roxytest-tests-lefse.R:15:3
 2.   └─rlang::cnd_signal(state$error)

[ FAIL 1 | WARN 0 | SKIP 9 | PASS 81 ]
Error: Test failures
Execution halted