R Under development (unstable) (2024-02-08 r85876 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 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(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: 5.21 MB in 15 files.

ℹ Updating metadata database
✔ Updating metadata database ... done

 
→ Will install 2 packages.
→ Will download 2 CRAN packages (5.91 MB).
+ abc        2.2.1 [dl] (1.00 MB)
+ abc.data   1.0   [dl] (4.91 MB)
ℹ Getting 2 pkgs (5.91 MB)
✔ Got abc.data 1.0 (i386+x86_64-w64-mingw32) (4.91 MB)
✔ Got abc 2.2.1 (i386+x86_64-w64-mingw32) (1.00 MB)
✔ Installed abc.data 1.0  (203ms)
✔ Installed abc 2.2.1  (124ms)
✔ 1 pkg + 10 deps: kept 9, added 2, dld 2 (5.91 MB) [28.7s]
[ FAIL 12 | WARN 1 | SKIP 2 | PASS 463 ]

══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• On CRAN (2): 'test_misc.R:103:3', 'test_figures_taxo.R:354:3'

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_cutadapt.R:17:5'): cutadapt_remove_primers works fine ────────
length(list.files(paste0(tempdir(), "/output_cutadapt"))) (`actual`) not equal to 2 (`expected`).

  `actual`: 0
`expected`: 2
── Failure ('test_cutadapt.R:37:5'): cutadapt_remove_primers works fine ────────
length(list.files(paste0(tempdir(), "/output_cutadapt"))) (`actual`) not equal to 2 (`expected`).

  `actual`: 0
`expected`: 2
── Failure ('test_cutadapt.R:55:5'): cutadapt_remove_primers works fine ────────
length(list.files(paste0(tempdir(), "/output_cutadapt"))) (`actual`) not equal to 2 (`expected`).

  `actual`: 0
`expected`: 2
── Error ('test_figures_beta_div.R:381:3'): multipatt_pq works with data_fungi_mini dataset ──
Error in `inDL(x, as.logical(local), as.logical(now), ...)`: unable to load shared object 'D:/RCompile/CRANpkg/lib/4.4/lme4/libs/x64/lme4.dll':
  `maximal number of DLLs reached...
Backtrace:
     ▆
  1. ├─testthat::expect_type(...) at test_figures_beta_div.R:381:3
  2. │ └─testthat::quasi_label(enquo(object), arg = "object")
  3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
  4. ├─base::suppressMessages(...)
  5. │ └─base::withCallingHandlers(...)
  6. ├─base::suppressWarnings(...)
  7. │ └─base::withCallingHandlers(...)
  8. ├─MiscMetabar::ancombc_pq(...)
  9. └─base::loadNamespace(x)
 10.   ├─base::namespaceImportFrom(...)
 11.   │ └─base::asNamespace(ns)
 12.   └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
 13.     └─base::library.dynam(lib, package, package.lib)
 14.       └─base::dyn.load(file, DLLpath = DLLpath, ...)
 15.         └─base (local) inDL(x, as.logical(local), as.logical(now), ...)
── Error ('test_phyloseq_class.R:93:3'): count_seq works fine ──────────────────
Error in `system(paste0("zcat ", file_path, " | grep -ce '^+$'"), intern = TRUE)`: 'zcat' not found
Backtrace:
    ▆
 1. ├─testthat::expect_equal(...) at test_phyloseq_class.R:93:3
 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
 3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
 4. └─MiscMetabar::count_seq("inst/extdata/ex_R1_001.fastq.gz")
 5.   └─base::system(...)
── Error ('test_figures_taxo.R:17:3'): rotl_pq works with data_fungi dataset ───
Error in `inDL(x, as.logical(local), as.logical(now), ...)`: unable to load shared object 'D:/RCompile/CRANpkg/lib/4.4/curl/libs/x64/curl.dll':
  `maximal number of DLLs reached...
Backtrace:
     ▆
  1. ├─testthat::expect_s3_class(...) at test_figures_taxo.R:17:3
  2. │ └─testthat::quasi_label(enquo(object), arg = "object")
  3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
  4. ├─base::suppressWarnings(tr <- rotl_pq(data_fungi, species_colnames = "Genus_species"))
  5. │ └─base::withCallingHandlers(...)
  6. ├─MiscMetabar::rotl_pq(data_fungi, species_colnames = "Genus_species")
  7. │ └─rotl::tnrs_match_names(taxa_names_rotl)
  8. │   ├─context_name %in% unlist(tnrs_contexts(...))
  9. │   ├─base::unlist(tnrs_contexts(...))
 10. │   └─rotl::tnrs_contexts(...)
 11. │     └─rotl:::.tnrs_contexts(...)
 12. │       └─rotl:::otl_POST("tnrs/contexts", body = list(), ...)
 13. │         └─rotl:::is_otl_online()
 14. └─base::loadNamespace(x)
 15.   └─base::library.dynam(lib, package, package.lib)
 16.     └─base::dyn.load(file, DLLpath = DLLpath, ...)
 17.       └─base (local) inDL(x, as.logical(local), as.logical(now), ...)
── Error ('test_figures_taxo.R:388:3'): build_phytree_pq work with data_fungi dataset ──
Error: package or namespace load failed for 'phangorn' in inDL(x, as.logical(local), as.logical(now), ...):
 unable to load shared object 'D:/RCompile/CRANpkg/lib/4.4/fastmatch/libs/x64/fastmatch.dll':
  `maximal number of DLLs reached...
Backtrace:
    ▆
 1. └─base::library("phangorn") at test_figures_taxo.R:388:3
 2.   └─base::tryCatch(...)
 3.     └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 4.       └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 5.         └─value[[3L]](cond)
── Error ('test_table_functions.R:5:3'): tax_datatable function works fine with data_fungi dataset ──
Error in `inDL(x, as.logical(local), as.logical(now), ...)`: unable to load shared object 'D:/RCompile/CRANpkg/lib/4.4/sass/libs/x64/sass.dll':
  `maximal number of DLLs reached...
Backtrace:
     ▆
  1. ├─testthat::expect_silent(taxdt <- tax_datatable(data_fungi)) at test_table_functions.R:5:3
  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::tax_datatable(data_fungi)
 10. │ ├─DT::datatable(df, ...) %>% ...
 11. │ └─DT::datatable(df, ...)
 12. │   └─DT:::normalizeStyle(style)
 13. ├─DT::formatStyle(...)
 14. │ └─DT:::formatColumns(...)
 15. └─base::loadNamespace(x)
 16.   ├─base::namespaceImport(...)
 17.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
 18.     └─base::library.dynam(lib, package, package.lib)
 19.       └─base::dyn.load(file, DLLpath = DLLpath, ...)
 20.         └─base (local) inDL(x, as.logical(local), as.logical(now), ...)
── Error ('test_table_functions.R:15:3'): tax_datatable function works fine with enterotype dataset ──
Error in `inDL(x, as.logical(local), as.logical(now), ...)`: unable to load shared object 'D:/RCompile/CRANpkg/lib/4.4/sass/libs/x64/sass.dll':
  `maximal number of DLLs reached...
Backtrace:
     ▆
  1. ├─testthat::expect_silent(tax_datatable(enterotype)) at test_table_functions.R:15:3
  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::tax_datatable(enterotype)
 10. │ ├─DT::datatable(df, ...) %>% ...
 11. │ └─DT::datatable(df, ...)
 12. │   └─DT:::normalizeStyle(style)
 13. ├─DT::formatStyle(...)
 14. │ └─DT:::formatColumns(...)
 15. └─base::loadNamespace(x)
 16.   ├─base::namespaceImport(...)
 17.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
 18.     └─base::library.dynam(lib, package, package.lib)
 19.       └─base::dyn.load(file, DLLpath = DLLpath, ...)
 20.         └─base (local) inDL(x, as.logical(local), as.logical(now), ...)
── Failure ('test_rw.R:40:3'): save_pq function works fine with data_fungi dataset ──
length(list.files(testFolder)) (`actual`) not equal to 6 (`expected`).

  `actual`: 12
`expected`:  6
── Error ('test_targets.R:81:3'): track_wkflow function works fine ─────────────
Error in `system(paste("zcat ", x, " | grep -c '^+$'", sep = ""), intern = TRUE)`: 'zcat' not found
Backtrace:
     ▆
  1. ├─testthat::expect_message(...) at test_targets.R:81:3
  2. │ └─testthat:::expect_condition_matching(...)
  3. │   └─testthat:::quasi_capture(...)
  4. │     ├─testthat (local) .capture(...)
  5. │     │ └─base::withCallingHandlers(...)
  6. │     └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  7. └─MiscMetabar::track_wkflow(...)
  8.   └─pbapply::pblapply(...)
  9.     └─base::lapply(X, FUN, ...)
 10.       └─MiscMetabar (local) FUN(X[[i]], ...)
 11.         └─pbapply::pbsapply(...)
 12.           └─pbapply::pblapply(X = X, FUN = FUN, ..., cl = cl)
 13.             └─base::lapply(X, FUN, ...)
 14.               └─MiscMetabar (local) FUN(X[[i]], ...)
 15.                 └─base::system(...)
── Error ('test_targets.R:122:3'): track_wkflow_samples function works fine with object of class matrix, dada and derep ──
Error in `system(paste("zcat ", x, " | grep -c '^+$'", sep = ""), intern = TRUE)`: 'zcat' not found
Backtrace:
     ▆
  1. ├─testthat::expect_s3_class(...) at test_targets.R:122:3
  2. │ └─testthat::quasi_label(enquo(object), arg = "object")
  3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
  4. └─MiscMetabar::track_wkflow(...)
  5.   └─pbapply::pblapply(...)
  6.     └─base::lapply(X, FUN, ...)
  7.       └─MiscMetabar (local) FUN(X[[i]], ...)
  8.         └─pbapply::pbsapply(...)
  9.           └─pbapply::pblapply(X = X, FUN = FUN, ..., cl = cl)
 10.             └─base::lapply(X, FUN, ...)
 11.               └─MiscMetabar (local) FUN(X[[i]], ...)
 12.                 └─base::system(...)

[ FAIL 12 | WARN 1 | SKIP 2 | PASS 463 ]
Error: Test failures
Execution halted