Last updated on 2025-09-13 06:49:33 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.3.1 | 16.11 | 142.66 | 158.77 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.3.1 | 11.41 | 101.13 | 112.54 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.3.1 | 245.10 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 1.3.1 | 226.74 | OK | |||
| r-devel-windows-x86_64 | 1.3.1 | 24.00 | 154.00 | 178.00 | OK | |
| r-patched-linux-x86_64 | 1.3.1 | 16.22 | 133.39 | 149.61 | ERROR | |
| r-release-linux-x86_64 | 1.3.1 | 14.92 | 132.28 | 147.20 | ERROR | |
| r-release-macos-arm64 | 1.3.1 | 62.00 | OK | |||
| r-release-macos-x86_64 | 1.3.1 | 107.00 | OK | |||
| r-release-windows-x86_64 | 1.3.1 | 16.00 | 132.00 | 148.00 | OK | |
| r-oldrel-macos-arm64 | 1.3.1 | 75.00 | OK | |||
| r-oldrel-macos-x86_64 | 1.3.1 | 94.00 | OK | |||
| r-oldrel-windows-x86_64 | 1.3.1 | 25.00 | 171.00 | 196.00 | ERROR |
Version: 1.3.1
Check: examples
Result: ERROR
Running examples in ‘OmicFlow-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: diversity_plot
> ### Title: Diversity plot
> ### Aliases: diversity_plot
>
> ### ** Examples
>
> library("ggplot2")
>
> n_row <- 1000
> n_col <- 100
> density <- 0.2
> num_entries <- n_row * n_col
> num_nonzero <- round(num_entries * density)
>
> set.seed(123)
> positions <- sample(num_entries, num_nonzero, replace=FALSE)
> row_idx <- ((positions - 1) %% n_row) + 1
> col_idx <- ((positions - 1) %/% n_row) + 1
>
> values <- runif(num_nonzero, min = 0, max = 1)
> sparse_mat <- Matrix::sparseMatrix(
+ i = row_idx,
+ j = col_idx,
+ x = values,
+ dims = c(n_row, n_col)
+ )
>
> div <- OmicFlow::diversity(
+ x = sparse_mat,
+ metric = "shannon"
+ )
>
> dt <- data.table::data.table(
+ "values" = div,
+ "treatment" = c(rep("healthy", n_col / 2), rep("tumor", n_col / 2))
+ )
>
> colors <- OmicFlow::colormap(dt, "treatment")
Warning in RColorBrewer::brewer.pal(length(unique_groups), Brewer.palID) :
minimal value for n is 3, returning requested palette with 3 different levels
>
> diversity_plot(
+ data = dt,
+ values = "values",
+ col_name = "treatment",
+ palette = colors,
+ method = "shannon",
+ paired = FALSE,
+ p.adjust.method = "fdr"
+ )
$plot
Error in `gghalves::geom_half_point_panel()`:
! Problem while converting geom to grob.
ℹ Error occurred in the 2nd layer.
Caused by error in `fun()`:
! argument "layout" is missing, with no default
Backtrace:
▆
1. ├─base (local) `<fn>`(x)
2. ├─ggplot2 (local) `print.ggplot2::ggplot`(x)
3. │ ├─ggplot2::ggplot_gtable(data)
4. │ └─ggplot2 (local) `ggplot_gtable.ggplot2::ggplot_built`(data)
5. │ └─ggplot2:::by_layer(...)
6. │ ├─rlang::try_fetch(...)
7. │ │ ├─base::tryCatch(...)
8. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
9. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
10. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
11. │ │ └─base::withCallingHandlers(...)
12. │ └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
13. │ └─l$draw_geom(d, layout)
14. │ └─ggplot2 (local) draw_geom(..., self = self)
15. │ └─self$geom$draw_layer(...)
16. │ └─ggplot2 (local) draw_layer(..., self = self)
17. │ └─base::lapply(...)
18. │ └─ggplot2 (local) FUN(X[[i]], ...)
19. │ ├─rlang::inject(self$draw_panel(data, panel_params, coord, !!!params))
20. │ └─self$draw_panel(...)
21. │ └─gghalves (local) draw_panel(...)
22. │ └─transformation$compute_layer(transformation_df, transformation_params)
23. │ └─ggplot2 (local) compute_layer(..., self = self)
24. │ └─ggplot2:::dapply(...)
25. │ └─base::lapply(...)
26. │ └─ggplot2 (local) FUN(X[[i]], ...)
27. │ └─ggplot2 (local) apply_fun(cur_data)
28. │ └─ggplot2 (local) fun(x, ...)
29. └─rlang (local) `<fn>`(`<gtvrErrr>`)
30. └─handlers[[1L]](cnd)
31. └─cli::cli_abort(...)
32. └─rlang::abort(...)
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 1.3.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [18s/24s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(ggplot2)
> library(OmicFlow)
Loading required package: R6
Loading required package: data.table
Loading required package: Matrix
> library(patchwork)
> set.seed(100)
> test_check("OmicFlow")
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
i Processing ... column: CONTRAST_sex
'nperm' >= set of all permutations: complete enumeration.
Set of permutations < 'minperm'. Generating entire set.
'nperm' >= set of all permutations: complete enumeration.
Set of permutations < 'minperm'. Generating entire set.
processing file: report.Rmd
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
'nperm' >= set of all permutations: complete enumeration.
Set of permutations < 'minperm'. Generating entire set.
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
[ FAIL 2 | WARN 0 | SKIP 9 | PASS 2 ]
══ Skipped tests (9) ═══════════════════════════════════════════════════════════
• On CRAN (9): 'test-alpha_diversity.R:15:3', 'test-composition.R:15:3',
'test-dfe.R:18:3', 'test-hill.R:12:3', 'test-metagenomics.R:15:3',
'test-ordination.R:17:3', 'test-subsetting.R:10:3',
'test-transformations.R:10:3', 'test-utils.R:15:5'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-autoflow.R:9:5'): Tests autoFlow report creation ───────────────
Error in `gghalves::geom_half_point_panel(aes(color = as.factor(.data[[col_name]])))`: Problem while converting geom to grob.
i Error occurred in the 2nd layer.
Caused by error in `fun()`:
! argument "layout" is missing, with no default
Backtrace:
▆
1. ├─base::suppressWarnings(taxa$autoFlow(filename = output_file)) at test-autoflow.R:9:5
2. │ └─base::withCallingHandlers(...)
3. ├─taxa$autoFlow(filename = output_file)
4. │ ├─rmarkdown::render(...)
5. │ │ └─knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
6. │ │ └─knitr:::process_file(text, output)
7. │ │ ├─xfun:::handle_error(...)
8. │ │ ├─base::withCallingHandlers(...)
9. │ │ └─knitr:::process_group(group)
10. │ │ └─knitr:::call_block(x)
11. │ │ └─knitr:::block_exec(params)
12. │ │ └─knitr:::eng_r(options)
13. │ │ ├─knitr:::in_input_dir(...)
14. │ │ │ └─knitr:::in_dir(input_dir(), expr)
15. │ │ └─knitr (local) evaluate(...)
16. │ │ └─evaluate::evaluate(...)
17. │ │ ├─base::withRestarts(...)
18. │ │ │ └─base (local) withRestartList(expr, restarts)
19. │ │ │ ├─base (local) withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
20. │ │ │ │ └─base (local) doWithOneRestart(return(expr), restart)
21. │ │ │ └─base (local) withRestartList(expr, restarts[-nr])
22. │ │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
23. │ │ │ └─base (local) doWithOneRestart(return(expr), restart)
24. │ │ ├─evaluate:::with_handlers(...)
25. │ │ │ ├─base::eval(call)
26. │ │ │ │ └─base::eval(call)
27. │ │ │ └─base::withCallingHandlers(...)
28. │ │ ├─base::withVisible(eval(expr, envir))
29. │ │ └─base::eval(expr, envir)
30. │ │ └─base::eval(expr, envir)
31. │ └─OmicFlow (local) create_plot_tabs(...)
32. │ ├─base::print(plots[[i]])
33. │ ├─base::print(plots[[i]])
34. │ └─ggplot2 (local) `print.ggplot2::ggplot`(plots[[i]])
35. │ ├─ggplot2::ggplot_gtable(data)
36. │ └─ggplot2 (local) `ggplot_gtable.ggplot2::ggplot_built`(data)
37. │ └─ggplot2:::by_layer(...)
38. │ ├─rlang::try_fetch(...)
39. │ │ ├─base::tryCatch(...)
40. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
41. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
42. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
43. │ │ └─base::withCallingHandlers(...)
44. │ └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
45. │ └─l$draw_geom(d, layout)
46. │ └─ggplot2 (local) draw_geom(..., self = self)
47. │ └─self$geom$draw_layer(...)
48. │ └─ggplot2 (local) draw_layer(..., self = self)
49. │ └─base::lapply(...)
50. │ └─ggplot2 (local) FUN(X[[i]], ...)
51. │ ├─rlang::inject(self$draw_panel(data, panel_params, coord, !!!params))
52. │ └─self$draw_panel(...)
53. │ └─gghalves (local) draw_panel(...)
54. │ └─transformation$compute_layer(transformation_df, transformation_params)
55. │ └─ggplot2 (local) compute_layer(..., self = self)
56. │ └─ggplot2:::dapply(...)
57. │ └─base::lapply(...)
58. │ └─ggplot2 (local) FUN(X[[i]], ...)
59. │ └─ggplot2 (local) apply_fun(cur_data)
60. │ └─ggplot2 (local) fun(x, ...)
61. └─rlang (local) `<fn>`(`<gtvrErrr>`)
62. └─handlers[[1L]](cnd)
63. └─cli::cli_abort(...)
64. └─rlang::abort(...)
── Error ('test-autoflow.R:9:5'): Tests autoFlow report creation ───────────────
Error in `file(con, "w")`: cannot open the connection
Backtrace:
▆
1. ├─base::suppressWarnings(taxa$autoFlow(filename = output_file)) at test-autoflow.R:9:5
2. │ └─base::withCallingHandlers(...)
3. └─taxa$autoFlow(filename = output_file)
4. └─rmarkdown::render(...)
5. └─knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
6. └─knitr:::process_file(text, output)
7. └─xfun:::handle_error(...)
8. └─knitr (local) handler(loc)
9. └─xfun::write_utf8(res, output %n% stdout())
10. └─base::writeLines(enc2utf8(text), con, ..., useBytes = TRUE)
11. └─base::file(con, "w")
[ FAIL 2 | WARN 0 | SKIP 9 | PASS 2 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.3.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [12s/14s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(ggplot2)
> library(OmicFlow)
Loading required package: R6
Loading required package: data.table
Loading required package: Matrix
> library(patchwork)
> set.seed(100)
> test_check("OmicFlow")
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
i Processing ... column: CONTRAST_sex
'nperm' >= set of all permutations: complete enumeration.
Set of permutations < 'minperm'. Generating entire set.
'nperm' >= set of all permutations: complete enumeration.
Set of permutations < 'minperm'. Generating entire set.
processing file: report.Rmd
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
'nperm' >= set of all permutations: complete enumeration.
Set of permutations < 'minperm'. Generating entire set.
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
[ FAIL 2 | WARN 0 | SKIP 9 | PASS 2 ]
══ Skipped tests (9) ═══════════════════════════════════════════════════════════
• On CRAN (9): 'test-alpha_diversity.R:15:3', 'test-composition.R:15:3',
'test-dfe.R:18:3', 'test-hill.R:12:3', 'test-metagenomics.R:15:3',
'test-ordination.R:17:3', 'test-subsetting.R:10:3',
'test-transformations.R:10:3', 'test-utils.R:15:5'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-autoflow.R:9:5'): Tests autoFlow report creation ───────────────
Error in `gghalves::geom_half_point_panel(aes(color = as.factor(.data[[col_name]])))`: Problem while converting geom to grob.
i Error occurred in the 2nd layer.
Caused by error in `fun()`:
! argument "layout" is missing, with no default
Backtrace:
▆
1. ├─base::suppressWarnings(taxa$autoFlow(filename = output_file)) at test-autoflow.R:9:5
2. │ └─base::withCallingHandlers(...)
3. ├─taxa$autoFlow(filename = output_file)
4. │ ├─rmarkdown::render(...)
5. │ │ └─knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
6. │ │ └─knitr:::process_file(text, output)
7. │ │ ├─xfun:::handle_error(...)
8. │ │ ├─base::withCallingHandlers(...)
9. │ │ └─knitr:::process_group(group)
10. │ │ └─knitr:::call_block(x)
11. │ │ └─knitr:::block_exec(params)
12. │ │ └─knitr:::eng_r(options)
13. │ │ ├─knitr:::in_input_dir(...)
14. │ │ │ └─knitr:::in_dir(input_dir(), expr)
15. │ │ └─knitr (local) evaluate(...)
16. │ │ └─evaluate::evaluate(...)
17. │ │ ├─base::withRestarts(...)
18. │ │ │ └─base (local) withRestartList(expr, restarts)
19. │ │ │ ├─base (local) withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
20. │ │ │ │ └─base (local) doWithOneRestart(return(expr), restart)
21. │ │ │ └─base (local) withRestartList(expr, restarts[-nr])
22. │ │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
23. │ │ │ └─base (local) doWithOneRestart(return(expr), restart)
24. │ │ ├─evaluate:::with_handlers(...)
25. │ │ │ ├─base::eval(call)
26. │ │ │ │ └─base::eval(call)
27. │ │ │ └─base::withCallingHandlers(...)
28. │ │ ├─base::withVisible(eval(expr, envir))
29. │ │ └─base::eval(expr, envir)
30. │ │ └─base::eval(expr, envir)
31. │ └─OmicFlow (local) create_plot_tabs(...)
32. │ ├─base::print(plots[[i]])
33. │ ├─base::print(plots[[i]])
34. │ └─ggplot2 (local) `print.ggplot2::ggplot`(plots[[i]])
35. │ ├─ggplot2::ggplot_gtable(data)
36. │ └─ggplot2 (local) `ggplot_gtable.ggplot2::ggplot_built`(data)
37. │ └─ggplot2:::by_layer(...)
38. │ ├─rlang::try_fetch(...)
39. │ │ ├─base::tryCatch(...)
40. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
41. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
42. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
43. │ │ └─base::withCallingHandlers(...)
44. │ └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
45. │ └─l$draw_geom(d, layout)
46. │ └─ggplot2 (local) draw_geom(..., self = self)
47. │ └─self$geom$draw_layer(...)
48. │ └─ggplot2 (local) draw_layer(..., self = self)
49. │ └─base::lapply(...)
50. │ └─ggplot2 (local) FUN(X[[i]], ...)
51. │ ├─rlang::inject(self$draw_panel(data, panel_params, coord, !!!params))
52. │ └─self$draw_panel(...)
53. │ └─gghalves (local) draw_panel(...)
54. │ └─transformation$compute_layer(transformation_df, transformation_params)
55. │ └─ggplot2 (local) compute_layer(..., self = self)
56. │ └─ggplot2:::dapply(...)
57. │ └─base::lapply(...)
58. │ └─ggplot2 (local) FUN(X[[i]], ...)
59. │ └─ggplot2 (local) apply_fun(cur_data)
60. │ └─ggplot2 (local) fun(x, ...)
61. └─rlang (local) `<fn>`(`<gtvrErrr>`)
62. └─handlers[[1L]](cnd)
63. └─cli::cli_abort(...)
64. └─rlang::abort(...)
── Error ('test-autoflow.R:9:5'): Tests autoFlow report creation ───────────────
Error in `file(con, "w")`: cannot open the connection
Backtrace:
▆
1. ├─base::suppressWarnings(taxa$autoFlow(filename = output_file)) at test-autoflow.R:9:5
2. │ └─base::withCallingHandlers(...)
3. └─taxa$autoFlow(filename = output_file)
4. └─rmarkdown::render(...)
5. └─knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
6. └─knitr:::process_file(text, output)
7. └─xfun:::handle_error(...)
8. └─knitr (local) handler(loc)
9. └─xfun::write_utf8(res, output %n% stdout())
10. └─base::writeLines(enc2utf8(text), con, ..., useBytes = TRUE)
11. └─base::file(con, "w")
[ FAIL 2 | WARN 0 | SKIP 9 | PASS 2 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.3.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [20s/27s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(ggplot2)
> library(OmicFlow)
Loading required package: R6
Loading required package: data.table
Loading required package: Matrix
> library(patchwork)
> set.seed(100)
> test_check("OmicFlow")
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
i Processing ... column: CONTRAST_sex
'nperm' >= set of all permutations: complete enumeration.
Set of permutations < 'minperm'. Generating entire set.
'nperm' >= set of all permutations: complete enumeration.
Set of permutations < 'minperm'. Generating entire set.
processing file: report.Rmd
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
'nperm' >= set of all permutations: complete enumeration.
Set of permutations < 'minperm'. Generating entire set.
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
[ FAIL 1 | WARN 0 | SKIP 9 | PASS 2 ]
══ Skipped tests (9) ═══════════════════════════════════════════════════════════
• On CRAN (9): 'test-alpha_diversity.R:15:3', 'test-composition.R:15:3',
'test-dfe.R:18:3', 'test-hill.R:12:3', 'test-metagenomics.R:15:3',
'test-ordination.R:17:3', 'test-subsetting.R:10:3',
'test-transformations.R:10:3', 'test-utils.R:15:5'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-autoflow.R:9:5'): Tests autoFlow report creation ───────────────
Error in `file(con, "w")`: cannot open the connection
Backtrace:
▆
1. ├─base::suppressWarnings(taxa$autoFlow(filename = output_file)) at test-autoflow.R:9:5
2. │ └─base::withCallingHandlers(...)
3. └─taxa$autoFlow(filename = output_file)
4. └─rmarkdown::render(...)
5. └─knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
6. └─xfun::write_utf8(res, output)
7. └─base::writeLines(enc2utf8(text), con, ..., useBytes = TRUE)
8. └─base::file(con, "w")
[ FAIL 1 | WARN 0 | SKIP 9 | PASS 2 ]
Error: Test failures
Execution halted
Flavor: r-patched-linux-x86_64
Version: 1.3.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [19s/23s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(ggplot2)
> library(OmicFlow)
Loading required package: R6
Loading required package: data.table
Loading required package: Matrix
> library(patchwork)
> set.seed(100)
> test_check("OmicFlow")
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
i Processing ... column: CONTRAST_sex
'nperm' >= set of all permutations: complete enumeration.
Set of permutations < 'minperm'. Generating entire set.
'nperm' >= set of all permutations: complete enumeration.
Set of permutations < 'minperm'. Generating entire set.
processing file: report.Rmd
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
'nperm' >= set of all permutations: complete enumeration.
Set of permutations < 'minperm'. Generating entire set.
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
[ FAIL 1 | WARN 0 | SKIP 9 | PASS 2 ]
══ Skipped tests (9) ═══════════════════════════════════════════════════════════
• On CRAN (9): 'test-alpha_diversity.R:15:3', 'test-composition.R:15:3',
'test-dfe.R:18:3', 'test-hill.R:12:3', 'test-metagenomics.R:15:3',
'test-ordination.R:17:3', 'test-subsetting.R:10:3',
'test-transformations.R:10:3', 'test-utils.R:15:5'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-autoflow.R:9:5'): Tests autoFlow report creation ───────────────
Error in `file(con, "w")`: cannot open the connection
Backtrace:
▆
1. ├─base::suppressWarnings(taxa$autoFlow(filename = output_file)) at test-autoflow.R:9:5
2. │ └─base::withCallingHandlers(...)
3. └─taxa$autoFlow(filename = output_file)
4. └─rmarkdown::render(...)
5. └─knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
6. └─xfun::write_utf8(res, output)
7. └─base::writeLines(enc2utf8(text), con, ..., useBytes = TRUE)
8. └─base::file(con, "w")
[ FAIL 1 | WARN 0 | SKIP 9 | PASS 2 ]
Error: Test failures
Execution halted
Flavor: r-release-linux-x86_64
Version: 1.3.1
Check: examples
Result: ERROR
Running examples in 'OmicFlow-Ex.R' failed
The error most likely occurred in:
> ### Name: diversity_plot
> ### Title: Diversity plot
> ### Aliases: diversity_plot
>
> ### ** Examples
>
> library("ggplot2")
>
> n_row <- 1000
> n_col <- 100
> density <- 0.2
> num_entries <- n_row * n_col
> num_nonzero <- round(num_entries * density)
>
> set.seed(123)
> positions <- sample(num_entries, num_nonzero, replace=FALSE)
> row_idx <- ((positions - 1) %% n_row) + 1
> col_idx <- ((positions - 1) %/% n_row) + 1
>
> values <- runif(num_nonzero, min = 0, max = 1)
> sparse_mat <- Matrix::sparseMatrix(
+ i = row_idx,
+ j = col_idx,
+ x = values,
+ dims = c(n_row, n_col)
+ )
>
> div <- OmicFlow::diversity(
+ x = sparse_mat,
+ metric = "shannon"
+ )
>
> dt <- data.table::data.table(
+ "values" = div,
+ "treatment" = c(rep("healthy", n_col / 2), rep("tumor", n_col / 2))
+ )
>
> colors <- OmicFlow::colormap(dt, "treatment")
Warning in RColorBrewer::brewer.pal(length(unique_groups), Brewer.palID) :
minimal value for n is 3, returning requested palette with 3 different levels
>
> diversity_plot(
+ data = dt,
+ values = "values",
+ col_name = "treatment",
+ palette = colors,
+ method = "shannon",
+ paired = FALSE,
+ p.adjust.method = "fdr"
+ )
$plot
Error in `gghalves::geom_half_point_panel()`:
! Problem while converting geom to grob.
ℹ Error occurred in the 2nd layer.
Caused by error in `fun()`:
! argument "layout" is missing, with no default
Backtrace:
▆
1. ├─base (local) `<fn>`(x)
2. ├─ggplot2 (local) `print.ggplot2::ggplot`(x)
3. │ ├─ggplot2::ggplot_gtable(data)
4. │ └─ggplot2 (local) `ggplot_gtable.ggplot2::ggplot_built`(data)
5. │ └─ggplot2:::by_layer(...)
6. │ ├─rlang::try_fetch(...)
7. │ │ ├─base::tryCatch(...)
8. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
9. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
10. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
11. │ │ └─base::withCallingHandlers(...)
12. │ └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
13. │ └─l$draw_geom(d, layout)
14. │ └─ggplot2 (local) draw_geom(..., self = self)
15. │ └─self$geom$draw_layer(...)
16. │ └─ggplot2 (local) draw_layer(..., self = self)
17. │ └─base::lapply(...)
18. │ └─ggplot2 (local) FUN(X[[i]], ...)
19. │ ├─rlang::inject(self$draw_panel(data, panel_params, coord, !!!params))
20. │ └─self$draw_panel(...)
21. │ └─gghalves (local) draw_panel(...)
22. │ └─transformation$compute_layer(transformation_df, transformation_params)
23. │ └─ggplot2 (local) compute_layer(..., self = self)
24. │ └─ggplot2:::dapply(...)
25. │ └─base::lapply(...)
26. │ └─ggplot2 (local) FUN(X[[i]], ...)
27. │ └─ggplot2 (local) apply_fun(cur_data)
28. │ └─ggplot2 (local) fun(x, ...)
29. └─base::.handleSimpleError(...)
30. └─rlang (local) h(simpleError(msg, call))
31. └─handlers[[1L]](cnd)
32. └─cli::cli_abort(...)
33. └─rlang::abort(...)
Execution halted
Flavor: r-oldrel-windows-x86_64
Version: 1.3.1
Check: tests
Result: ERROR
Running 'testthat.R' [16s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(ggplot2)
> library(OmicFlow)
Loading required package: R6
Loading required package: data.table
Loading required package: Matrix
> library(patchwork)
> set.seed(100)
> test_check("OmicFlow")
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
i Processing ... column: CONTRAST_sex
'nperm' >= set of all permutations: complete enumeration.
Set of permutations < 'minperm'. Generating entire set.
'nperm' >= set of all permutations: complete enumeration.
Set of permutations < 'minperm'. Generating entire set.
processing file: report.Rmd
Quitting from report.Rmd:161-173 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NULL
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
'nperm' >= set of all permutations: complete enumeration.
Set of permutations < 'minperm'. Generating entire set.
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
[ FAIL 1 | WARN 0 | SKIP 9 | PASS 2 ]
══ Skipped tests (9) ═══════════════════════════════════════════════════════════
• On CRAN (9): 'test-alpha_diversity.R:15:3', 'test-composition.R:15:3',
'test-dfe.R:18:3', 'test-hill.R:12:3', 'test-metagenomics.R:15:3',
'test-ordination.R:17:3', 'test-subsetting.R:10:3',
'test-transformations.R:10:3', 'test-utils.R:15:5'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-autoflow.R:9:5'): Tests autoFlow report creation ───────────────
Error in `gghalves::geom_half_point_panel(aes(color = as.factor(.data[[col_name]])))`: Problem while converting geom to grob.
i Error occurred in the 2nd layer.
Caused by error in `fun()`:
! argument "layout" is missing, with no default
Backtrace:
▆
1. ├─base::suppressWarnings(taxa$autoFlow(filename = output_file)) at test-autoflow.R:9:5
2. │ └─base::withCallingHandlers(...)
3. ├─taxa$autoFlow(filename = output_file)
4. │ ├─rmarkdown::render(...)
5. │ │ └─knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
6. │ │ └─knitr:::process_file(text, output)
7. │ │ ├─xfun:::handle_error(...)
8. │ │ ├─base::withCallingHandlers(...)
9. │ │ └─knitr:::process_group(group)
10. │ │ └─knitr:::call_block(x)
11. │ │ └─knitr:::block_exec(params)
12. │ │ └─knitr:::eng_r(options)
13. │ │ ├─knitr:::in_input_dir(...)
14. │ │ │ └─knitr:::in_dir(input_dir(), expr)
15. │ │ └─knitr (local) evaluate(...)
16. │ │ └─evaluate::evaluate(...)
17. │ │ ├─base::withRestarts(...)
18. │ │ │ └─base (local) withRestartList(expr, restarts)
19. │ │ │ ├─base (local) withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
20. │ │ │ │ └─base (local) doWithOneRestart(return(expr), restart)
21. │ │ │ └─base (local) withRestartList(expr, restarts[-nr])
22. │ │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
23. │ │ │ └─base (local) doWithOneRestart(return(expr), restart)
24. │ │ ├─evaluate:::with_handlers(...)
25. │ │ │ ├─base::eval(call)
26. │ │ │ │ └─base::eval(call)
27. │ │ │ └─base::withCallingHandlers(...)
28. │ │ ├─base::withVisible(eval(expr, envir))
29. │ │ └─base::eval(expr, envir)
30. │ │ └─base::eval(expr, envir)
31. │ └─OmicFlow (local) create_plot_tabs(...)
32. │ ├─base::print(plots[[i]])
33. │ ├─base::print(plots[[i]])
34. │ └─ggplot2 (local) `print.ggplot2::ggplot`(plots[[i]])
35. │ ├─ggplot2::ggplot_gtable(data)
36. │ └─ggplot2 (local) `ggplot_gtable.ggplot2::ggplot_built`(data)
37. │ └─ggplot2:::by_layer(...)
38. │ ├─rlang::try_fetch(...)
39. │ │ ├─base::tryCatch(...)
40. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
41. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
42. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
43. │ │ └─base::withCallingHandlers(...)
44. │ └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
45. │ └─l$draw_geom(d, layout)
46. │ └─ggplot2 (local) draw_geom(..., self = self)
47. │ └─self$geom$draw_layer(...)
48. │ └─ggplot2 (local) draw_layer(..., self = self)
49. │ └─base::lapply(...)
50. │ └─ggplot2 (local) FUN(X[[i]], ...)
51. │ ├─rlang::inject(self$draw_panel(data, panel_params, coord, !!!params))
52. │ └─self$draw_panel(...)
53. │ └─gghalves (local) draw_panel(...)
54. │ └─transformation$compute_layer(transformation_df, transformation_params)
55. │ └─ggplot2 (local) compute_layer(..., self = self)
56. │ └─ggplot2:::dapply(...)
57. │ └─base::lapply(...)
58. │ └─ggplot2 (local) FUN(X[[i]], ...)
59. │ └─ggplot2 (local) apply_fun(cur_data)
60. │ └─ggplot2 (local) fun(x, ...)
61. └─base::.handleSimpleError(...)
62. └─rlang (local) h(simpleError(msg, call))
63. └─handlers[[1L]](cnd)
64. └─cli::cli_abort(...)
65. └─rlang::abort(...)
[ FAIL 1 | WARN 0 | SKIP 9 | PASS 2 ]
Error: Test failures
Execution halted
Flavor: r-oldrel-windows-x86_64