Last updated on 2025-09-11 21:50:56 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.14.3 | 61.98 | 730.21 | 792.19 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.14.3 | 41.50 | 530.72 | 572.22 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.14.3 | 1265.84 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 0.14.3 | 1205.47 | ERROR | |||
| r-devel-windows-x86_64 | 0.14.3 | 59.00 | 695.00 | 754.00 | OK | |
| r-patched-linux-x86_64 | 0.14.3 | 62.04 | 694.87 | 756.91 | OK | |
| r-release-linux-x86_64 | 0.14.3 | 57.16 | 691.82 | 748.98 | OK | |
| r-release-macos-arm64 | 0.14.3 | 261.00 | OK | |||
| r-release-macos-x86_64 | 0.14.3 | 434.00 | OK | |||
| r-release-windows-x86_64 | 0.14.3 | 59.00 | 698.00 | 757.00 | OK | |
| r-oldrel-macos-arm64 | 0.14.3 | 295.00 | OK | |||
| r-oldrel-macos-x86_64 | 0.14.3 | 463.00 | NOTE | |||
| r-oldrel-windows-x86_64 | 0.14.3 | 77.00 | 945.00 | 1022.00 | OK |
Version: 0.14.3
Check: tests
Result: ERROR
Running ‘spelling.R’ [0s/1s]
Running ‘testthat.R’ [81s/54s]
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
Loading required package: purrr
Attaching package: 'purrr'
The following object is masked from 'package:testthat':
is_null
>
> test_check("MiscMetabar")
Starting 2 test processes
[ FAIL 1 | WARN 2 | SKIP 74 | PASS 82 ]
══ Skipped tests (74) ══════════════════════════════════════════════════════════
• On CRAN (74): 'test_adonis.R:1:1', 'test_controls.R:7:3',
'test_controls.R:14:3', 'test_controls.R:46:3', 'test_deprecated.R:1:1',
'test_clean_pq.R:8:3', 'test_clean_pq.R:17:3',
'test_figures_alpha_div.R:17:3', 'test_figures_alpha_div.R:63:3',
'test_figures_alpha_div.R:73:3', 'test_figures_alpha_div.R:95:3',
'test_figures_alpha_div.R:122:3', 'test_figures_alpha_div.R:151:3',
'test_figures_alpha_div.R:157:3', 'test_deseq2_edgeR.R:16:5',
'test_deseq2_edgeR.R:25:3', 'test_deseq2_edgeR.R:48:5',
'test_deseq2_edgeR.R:59:3', 'test_figures_biplot.R:14:3',
'test_figures_biplot.R:52:3', 'test_figures_misc.R:11:3',
'test_figures_misc.R:19:3', 'test_figures_misc.R:26:3',
'test_figures_misc.R:35:3', 'test_figures_summary_plot.R:9:3',
'test_figures_summary_plot.R:19:3', 'test_figures_summary_plot.R:28:3',
'test_figures_beta_div.R:22:3', 'test_figures_beta_div.R:73:5',
'test_figures_beta_div.R:92:3', 'test_figures_beta_div.R:102:5',
'test_figures_beta_div.R:159:5', 'test_figures_beta_div.R:209:3',
'test_figures_beta_div.R:241:5', 'test_figures_beta_div.R:259:5',
'test_figures_beta_div.R:289:5', 'test_figures_beta_div.R:314:3',
'test_figures_beta_div.R:346:3', 'test_figures_beta_div.R:355:3',
'test_figures_beta_div.R:387:3', 'test_figures_beta_div.R:402:3',
'test_figures_beta_div.R:414:3', 'test_krona.R:7:3',
'test_figures_taxo.R:64:3', 'test_figures_taxo.R:165:3',
'test_figures_taxo.R:209:5', 'test_figures_taxo.R:252:5',
'test_figures_taxo.R:319:5', 'test_figures_taxo.R:354:3',
'test_figures_taxo.R:379:3', 'test_figures_taxo.R:414:3',
'test_phyloseq_class.R:10:3', 'test_phyloseq_class.R:51:3',
'test_phyloseq_class.R:95:3', 'test_rw.R:8:3', 'test_rw.R:24:3',
'test_rw.R:39:3', 'test_subset.R:7:3', 'test_subset.R:18:3',
'test_table_functions.R:6:3', 'test_table_functions.R:19:3',
'test_table_functions.R:34:5', 'test_table_functions.R:47:5',
'test_targets.R:5:3', 'test_targets.R:56:3', 'test_targets.R:84:3',
'test_targets.R:101:3', 'test_targets.R:111:3', 'test_tuckey.R:5:3',
'test_tuckey.R:17:3', 'test_tuckey.R:26:3', 'test_misc.R:11:3',
'test_misc.R:30:3', 'test_misc.R:97:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_figures_beta_div.R:72:5'): graph_test_pq works ───────────────
`graph_test_pq(data_fungi_mini, fact = "Tree_name")` produced warnings.
[ FAIL 1 | WARN 2 | SKIP 74 | PASS 82 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.14.3
Check: examples
Result: ERROR
Running examples in ‘MiscMetabar-Ex.R’ failed
The error most likely occurred in:
> ### Name: upset_pq
> ### Title: Make upset plot for phyloseq object.
> ### Aliases: upset_pq
>
> ### ** Examples
>
> if (requireNamespace("ComplexUpset")) {
+ upset_pq(data_fungi_mini,
+ fact = "Height", width_ratio = 0.2,
+ taxa_fill = "Class"
+ )
+ }
Loading required namespace: ComplexUpset
Cleaning suppress 0 taxa ( ) and 0 sample(s) ( ).
Number of non-matching ASV 0
Number of matching ASV 45
Number of filtered-out ASV 0
Number of kept ASV 45
Number of kept samples 137
Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead.
ℹ The deprecated feature was likely used in the ComplexUpset package.
Please report the issue at
<https://github.com/krassowski/complex-upset/issues>.
Warning: themes$intersections_matrix is not a valid theme.
Please use `theme()` to construct themes.
Warning: `legend.margin` must be specified using `margin()`
ℹ For the old behavior use `legend.spacing`
Warning: themes$intersections_matrix is not a valid theme.
Please use `theme()` to construct themes.
Warning: selected_theme is not a valid theme.
Please use `theme()` to construct themes.
Warning: `legend.margin` must be specified using `margin()`
ℹ For the old behavior use `legend.spacing`
Warning: selected_theme is not a valid theme.
Please use `theme()` to construct themes.
Error in `method(update_ggplot, list(ggplot2::theme, ggplot2::ggplot))`:
! Can't merge the `axis.text` theme element.
Caused by error:
! `object` must be an <S7_object>, not a S3<element_text/element>
Backtrace:
▆
1. ├─MiscMetabar::upset_pq(...)
2. │ └─ComplexUpset::upset(...)
3. │ └─S7:::Ops.S7_object(...)
4. │ ├─base::tryCatch(return(base_ops[[.Generic]](e1, e2)), S7_error_method_not_found = function(cnd) cnd)
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_ops[[.Generic]](e1, e2)
9. │ ├─S7::S7_dispatch()
10. │ └─ggplot2 (local) `method(+, list(ggplot2::ggplot, class_any))`(...)
11. │ └─ggplot2:::add_ggplot(e1, e2, e2name)
12. │ ├─ggplot2::ggplot_add(object, p, objectname)
13. │ └─ggplot2:::ggplot_add.default(object, p, objectname)
14. │ └─ggplot2::update_ggplot(object = object, plot = plot, ...)
15. │ ├─S7::S7_dispatch()
16. │ └─ggplot2 (local) `method(update_ggplot, list(ggplot2::theme, ggplot2::ggplot))`(object = `<theme>`, plot = `<ggplt2::>`, ...)
17. │ ├─S7::set_props(plot, theme = add_theme(plot@theme, object))
18. │ └─ggplot2:::add_theme(plot@theme, object)
19. │ ├─rlang::try_fetch(...)
20. │ │ ├─base::tryCatch(...)
21. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
22. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
23. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
24. │ │ └─base::withCallingHandlers(...)
25. │ └─ggplot2::merge_element(t2[[item]], t1[[item]])
26. │ ├─S7::S7_dispatch()
27. │ └─ggplot2 (local) `method(merge_element, list(ggplot2::element, class_any))`(...)
28. │ └─S7::props(old, idx)
29. │ └─S7::check_is_S7(object)
30. │ └─base::stop(msg, call. = FALSE)
31. └─base::.handleSimpleError(...)
32. └─rlang (local) h(simpleError(msg, call))
33. └─handlers[[1L]](cnd)
34. └─cli::cli_abort(...)
35. └─rlang::abort(...)
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 0.14.3
Check: tests
Result: ERROR
Running ‘spelling.R’
Running ‘testthat.R’ [189s/143s]
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
Loading required package: purrr
Attaching package: 'purrr'
The following object is masked from 'package:testthat':
is_null
>
> test_check("MiscMetabar")
Starting 2 test processes
[ FAIL 2 | WARN 2 | SKIP 74 | PASS 81 ]
══ Skipped tests (74) ══════════════════════════════════════════════════════════
• On CRAN (74): 'test_adonis.R:1:1', 'test_controls.R:7:3',
'test_controls.R:14:3', 'test_controls.R:46:3', 'test_deprecated.R:1:1',
'test_clean_pq.R:8:3', 'test_clean_pq.R:17:3',
'test_figures_alpha_div.R:17:3', 'test_figures_alpha_div.R:63:3',
'test_figures_alpha_div.R:73:3', 'test_figures_alpha_div.R:95:3',
'test_figures_alpha_div.R:122:3', 'test_figures_alpha_div.R:151:3',
'test_figures_alpha_div.R:157:3', 'test_deseq2_edgeR.R:16:5',
'test_deseq2_edgeR.R:25:3', 'test_deseq2_edgeR.R:48:5',
'test_deseq2_edgeR.R:59:3', 'test_figures_biplot.R:14:3',
'test_figures_biplot.R:52:3', 'test_figures_misc.R:11:3',
'test_figures_misc.R:19:3', 'test_figures_misc.R:26:3',
'test_figures_misc.R:35:3', 'test_figures_summary_plot.R:9:3',
'test_figures_summary_plot.R:19:3', 'test_figures_summary_plot.R:28:3',
'test_figures_beta_div.R:22:3', 'test_figures_beta_div.R:73:5',
'test_figures_beta_div.R:92:3', 'test_figures_beta_div.R:102:5',
'test_figures_beta_div.R:159:5', 'test_figures_beta_div.R:209:3',
'test_figures_beta_div.R:241:5', 'test_figures_beta_div.R:259:5',
'test_figures_beta_div.R:289:5', 'test_figures_beta_div.R:314:3',
'test_figures_beta_div.R:346:3', 'test_figures_beta_div.R:355:3',
'test_figures_beta_div.R:387:3', 'test_figures_beta_div.R:402:3',
'test_figures_beta_div.R:414:3', 'test_krona.R:7:3',
'test_figures_taxo.R:64:3', 'test_figures_taxo.R:165:3',
'test_figures_taxo.R:209:5', 'test_figures_taxo.R:252:5',
'test_figures_taxo.R:319:5', 'test_figures_taxo.R:354:3',
'test_figures_taxo.R:379:3', 'test_figures_taxo.R:414:3',
'test_phyloseq_class.R:10:3', 'test_phyloseq_class.R:51:3',
'test_phyloseq_class.R:95:3', 'test_rw.R:8:3', 'test_rw.R:24:3',
'test_rw.R:39:3', 'test_subset.R:7:3', 'test_subset.R:18:3',
'test_table_functions.R:6:3', 'test_table_functions.R:19:3',
'test_table_functions.R:34:5', 'test_table_functions.R:47:5',
'test_targets.R:5:3', 'test_targets.R:56:3', 'test_targets.R:84:3',
'test_targets.R:101:3', 'test_targets.R:111:3', 'test_tuckey.R:5:3',
'test_tuckey.R:17:3', 'test_tuckey.R:26:3', 'test_misc.R:11:3',
'test_misc.R:30:3', 'test_misc.R:97:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_figures_beta_div.R:72:5'): graph_test_pq works ───────────────
`graph_test_pq(data_fungi_mini, fact = "Tree_name")` produced warnings.
── Failure ('test_figures_beta_div.R:258:5'): upset_pq works with data_fungi dataset ──
`suppressMessages(upset_pq(data_fungi_mini, "Height"))` produced warnings.
[ FAIL 2 | WARN 2 | SKIP 74 | PASS 81 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.14.3
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘MiscMetabar.Rmd’ using rmarkdown
Quitting from MiscMetabar.Rmd:66-68 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NULL
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'MiscMetabar.Rmd' failed with diagnostics:
Can't merge the `axis.text` theme element.
Caused by error:
! `object` must be an <S7_object>, not a S3<element_text/element>
--- failed re-building ‘MiscMetabar.Rmd’
SUMMARY: processing the following file failed:
‘MiscMetabar.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 0.14.3
Check: tests
Result: ERROR
Running ‘spelling.R’
Running ‘testthat.R’ [181s/137s]
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
Loading required package: purrr
Attaching package: 'purrr'
The following object is masked from 'package:testthat':
is_null
>
> test_check("MiscMetabar")
Starting 2 test processes
[ FAIL 2 | WARN 2 | SKIP 74 | PASS 81 ]
══ Skipped tests (74) ══════════════════════════════════════════════════════════
• On CRAN (74): 'test_adonis.R:1:1', 'test_controls.R:7:3',
'test_controls.R:14:3', 'test_controls.R:46:3', 'test_deprecated.R:1:1',
'test_clean_pq.R:8:3', 'test_clean_pq.R:17:3',
'test_figures_alpha_div.R:17:3', 'test_figures_alpha_div.R:63:3',
'test_figures_alpha_div.R:73:3', 'test_figures_alpha_div.R:95:3',
'test_figures_alpha_div.R:122:3', 'test_figures_alpha_div.R:151:3',
'test_figures_alpha_div.R:157:3', 'test_deseq2_edgeR.R:16:5',
'test_deseq2_edgeR.R:25:3', 'test_deseq2_edgeR.R:48:5',
'test_deseq2_edgeR.R:59:3', 'test_figures_biplot.R:14:3',
'test_figures_biplot.R:52:3', 'test_figures_misc.R:11:3',
'test_figures_misc.R:19:3', 'test_figures_misc.R:26:3',
'test_figures_misc.R:35:3', 'test_figures_summary_plot.R:9:3',
'test_figures_summary_plot.R:19:3', 'test_figures_summary_plot.R:28:3',
'test_figures_beta_div.R:22:3', 'test_figures_beta_div.R:73:5',
'test_figures_beta_div.R:92:3', 'test_figures_beta_div.R:102:5',
'test_figures_beta_div.R:159:5', 'test_figures_beta_div.R:209:3',
'test_figures_beta_div.R:241:5', 'test_figures_beta_div.R:259:5',
'test_figures_beta_div.R:289:5', 'test_figures_beta_div.R:314:3',
'test_figures_beta_div.R:346:3', 'test_figures_beta_div.R:355:3',
'test_figures_beta_div.R:387:3', 'test_figures_beta_div.R:402:3',
'test_figures_beta_div.R:414:3', 'test_figures_taxo.R:64:3',
'test_figures_taxo.R:165:3', 'test_figures_taxo.R:209:5',
'test_figures_taxo.R:252:5', 'test_figures_taxo.R:319:5',
'test_figures_taxo.R:354:3', 'test_figures_taxo.R:379:3',
'test_figures_taxo.R:414:3', 'test_krona.R:7:3',
'test_phyloseq_class.R:10:3', 'test_phyloseq_class.R:51:3',
'test_phyloseq_class.R:95:3', 'test_rw.R:8:3', 'test_rw.R:24:3',
'test_rw.R:39:3', 'test_subset.R:7:3', 'test_subset.R:18:3',
'test_table_functions.R:6:3', 'test_table_functions.R:19:3',
'test_table_functions.R:34:5', 'test_table_functions.R:47:5',
'test_targets.R:5:3', 'test_targets.R:56:3', 'test_targets.R:84:3',
'test_targets.R:101:3', 'test_targets.R:111:3', 'test_tuckey.R:5:3',
'test_tuckey.R:17:3', 'test_tuckey.R:26:3', 'test_misc.R:11:3',
'test_misc.R:30:3', 'test_misc.R:97:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_figures_beta_div.R:72:5'): graph_test_pq works ───────────────
`graph_test_pq(data_fungi_mini, fact = "Tree_name")` produced warnings.
── Failure ('test_figures_beta_div.R:258:5'): upset_pq works with data_fungi dataset ──
`suppressMessages(upset_pq(data_fungi_mini, "Height"))` produced warnings.
[ FAIL 2 | WARN 2 | SKIP 74 | PASS 81 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.14.3
Check: package dependencies
Result: NOTE
Packages suggested but not available for checking: 'ANCOMBC', 'mia'
Flavor: r-oldrel-macos-x86_64
Version: 0.14.3
Check: Rd cross-references
Result: NOTE
Package unavailable to check Rd xrefs: ‘ANCOMBC’
Flavor: r-oldrel-macos-x86_64