* using log directory ‘/srv/hornik/tmp/CRAN/MiscMetabar.Rcheck’
* using R Under development (unstable) (2024-02-07 r85873)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 17.0.6 (5)
    Debian flang-new version 17.0.6 (5)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘MiscMetabar/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MiscMetabar’ version ‘0.7.3’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [5s/9s] NOTE
Maintainer: ‘Adrien Taudière <adrien.taudiere@zaclys.net>’

New submission

Possibly misspelled words in DESCRIPTION:
  Metabarcoding (3:36)
  MiscMetabar (7:18, 7:205, 7:284)
  bioinformatic (7:255)
  dada (7:187)
  metabarcoding (7:126)
  phyloseq (7:177)
  powerfull (7:360)
  reproducibility (7:107)

Found the following (possibly) invalid URLs:
  URL: 
    From: inst/doc/MiscMetabar.html
    Message: Empty URL
  URL: https://github.com/torognes/vsearch/releases/download/v2.23.0/vsearch_manual.pdf
    From: man/asv2otu.Rd
          man/vsearch_clustering.Rd
    Status: 401
    Message: Unauthorized

Found the following (possibly) invalid file URI:
  URI: code_of_conduct.md
    From: README.md

Found the following (possibly) invalid DOIs:
  DOI: 10.7717/2Fpeerj.593
    From: man/swarm_clustering.Rd
    Status: 404
    Message: Not Found
* 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 executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MiscMetabar’ can be installed ... [26s/26s] OK
* checking package directory ... OK
* checking for future file timestamps ... 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [7s/7s] OK
* checking whether the package can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the package can be unloaded cleanly ... [7s/7s] OK
* checking whether the namespace can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the namespace can be unloaded cleanly ... [7s/7s] OK
* checking loading without being on the library search path ... [7s/7s] OK
* checking use of S3 registration ... 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 ... [35s/35s] OK
* checking Rd files ... [1s/1s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 ... [4s/4s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [240s/244s] ERROR
Running examples in ‘MiscMetabar-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: vsearch_clustering
> ### Title: Recluster sequences of an object of class 'physeq' or cluster a
> ###   list of DNA sequences using vsearch software
> ### Aliases: vsearch_clustering
> 
> ### ** Examples
> 
> 
> summary_plot_pq(data_fungi)
Cleaning suppress 0 taxa and 0 samples.
> d_vs <- vsearch_clustering(data_fungi)
Error in system2(vsearchpath, paste0(paste0(" ", vsearch_cluster_method,  : 
  error in running command
Calls: vsearch_clustering -> system2
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [20m/11m] ERROR
  Running ‘testthat.R’ [20m/11m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(MiscMetabar)
  Loading required package: phyloseq
  Loading required package: ggplot2
  Loading required package: dada2
  Loading required package: Rcpp
  Loading required package: dplyr
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  > 
  > test_check("MiscMetabar")
  Starting 2 test processes
  
  ✔ Updated metadata database: 2.88 MB in 8 files.
  
  ℹ Updating metadata database
  ✔ Updating metadata database ... done
  
   
  → Will install 2 packages.
  → Will download 2 CRAN packages (5.76 MB).
  + abc        2.2.1 [bld][dl] (869.83 kB)
  + abc.data   1.0   [bld][dl] (4.89 MB)
    
  ℹ Getting 2 pkgs (5.76 MB)
  ✔ Got abc 2.2.1 (source) (869.83 kB)
  ✔ Got abc.data 1.0 (source) (4.89 MB)
  ℹ Building abc.data 1.0
  ✔ Built abc.data 1.0 (849ms)
  ✔ Installed abc.data 1.0  (1s)
  ℹ Building abc 2.2.1
  ✔ Built abc 2.2.1 (3.3s)
  ✔ Installed abc 2.2.1  (1s)
  ✔ 1 pkg + 10 deps: kept 9, added 2, dld 2 (5.76 MB) [21s]
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 499 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_misc.R:104:3'): add_funguild_info works fine ───────────────────
  <purrr_error_indexed/rlang_error/error/condition>
  Error in `map(.x, .f, ...)`: i In index: 1.
  Caused by error:
  ! lexical error: invalid char in json text.
                                         </body>
                       (right here) ------^
  Backtrace:
       ▆
    1. ├─testthat::expect_silent(...) at test_misc.R:104:3
    2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ ├─withr::with_output_sink(...)
    5. │   │ │ └─base::force(code)
    6. │   │ ├─base::withCallingHandlers(...)
    7. │   │ └─base::withVisible(code)
    8. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    9. ├─MiscMetabar::add_funguild_info(...)
   10. │ └─MiscMetabar::funguild_assign(...)
   11. │   ├─dplyr::mutate(...)
   12. │   └─MiscMetabar::get_funguild_db()
   13. │     └─... %>% ...
   14. ├─dplyr::select(...)
   15. ├─purrr::map_dfr(...)
   16. │ └─purrr::map(.x, .f, ...)
   17. │   └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
   18. │     ├─purrr:::with_indexed_errors(...)
   19. │     │ └─base::withCallingHandlers(...)
   20. │     ├─purrr:::call_with_cleanup(...)
   21. │     └─MiscMetabar (local) .f(.x[[i]], ...)
   22. │       └─jsonlite::fromJSON(record)
   23. │         └─jsonlite:::parse_and_simplify(...)
   24. │           └─jsonlite:::parseJSON(txt, bigint_as_char)
   25. │             └─jsonlite:::parse_string(txt, bigint_as_char)
   26. └─base::.handleSimpleError(...)
   27.   └─purrr (local) h(simpleError(msg, call))
   28.     └─cli::cli_abort(...)
   29.       └─rlang::abort(...)
  ── Error ('test_figures_taxo.R:364:3'): add_funguild_info and plot_guild_pq work with data_fungi dataset ──
  <purrr_error_indexed/rlang_error/error/condition>
  Error in `map(.x, .f, ...)`: i In index: 1.
  Caused by error:
  ! lexical error: invalid char in json text.
                                         </body>
                       (right here) ------^
  Backtrace:
       ▆
    1. ├─testthat::expect_s4_class(...) at test_figures_taxo.R:364:3
    2. │ └─testthat::quasi_label(enquo(object), arg = "object")
    3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    4. ├─MiscMetabar::add_funguild_info(...)
    5. │ └─MiscMetabar::funguild_assign(...)
    6. │   ├─dplyr::mutate(...)
    7. │   └─MiscMetabar::get_funguild_db()
    8. │     └─... %>% ...
    9. ├─dplyr::select(...)
   10. ├─purrr::map_dfr(...)
   11. │ └─purrr::map(.x, .f, ...)
   12. │   └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
   13. │     ├─purrr:::with_indexed_errors(...)
   14. │     │ └─base::withCallingHandlers(...)
   15. │     ├─purrr:::call_with_cleanup(...)
   16. │     └─MiscMetabar (local) .f(.x[[i]], ...)
   17. │       └─jsonlite::fromJSON(record)
   18. │         └─jsonlite:::parse_and_simplify(...)
   19. │           └─jsonlite:::parseJSON(txt, bigint_as_char)
   20. │             └─jsonlite:::parse_string(txt, bigint_as_char)
   21. └─base::.handleSimpleError(...)
   22.   └─purrr (local) h(simpleError(msg, call))
   23.     └─cli::cli_abort(...)
   24.       └─rlang::abort(...)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 499 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [12s/12s] OK
* checking PDF version of manual ... [5s/5s] OK
* checking HTML version of manual ... [2s/2s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 2 ERRORs, 1 NOTE