Last updated on 2025-09-12 01:52:53 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.1.1 | 3.52 | 195.50 | 199.02 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.1.1 | 2.73 | 120.65 | 123.38 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.1.1 | 311.79 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 0.1.1 | 304.68 | OK | |||
| r-devel-windows-x86_64 | 0.1.1 | 7.00 | 181.00 | 188.00 | OK | |
| r-patched-linux-x86_64 | 0.1.1 | 3.70 | 183.65 | 187.35 | OK | |
| r-release-linux-x86_64 | 0.1.1 | 3.64 | 184.40 | 188.04 | OK | |
| r-release-macos-arm64 | 0.1.1 | 66.00 | OK | |||
| r-release-macos-x86_64 | 0.1.1 | 165.00 | OK | |||
| r-release-windows-x86_64 | 0.1.1 | 7.00 | 173.00 | 180.00 | OK | |
| r-oldrel-macos-arm64 | 0.1.1 | 86.00 | OK | |||
| r-oldrel-macos-x86_64 | 0.1.1 | 203.00 | OK | |||
| r-oldrel-windows-x86_64 | 0.1.1 | 10.00 | 235.00 | 245.00 | OK |
Version: 0.1.1
Check: examples
Result: ERROR
Running examples in ‘readyomics-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ready_plots
> ### Title: Generate plots from a differential analysis ('dana') object
> ### Aliases: ready_plots
>
> ### ** Examples
>
> set.seed(123)
> mock_X <- matrix(rnorm(20 * 5), nrow = 20)
> colnames(mock_X) <- paste0("feat_", seq_len(5))
> rownames(mock_X) <- paste0("sample_", seq_len(20))
>
> sample_data <- data.frame(
+ sample_id = rownames(mock_X),
+ group = factor(rep(c("A", "B"), each = 10)),
+ time = factor(rep(c("T1", "T2"), times = 10)),
+ subject_id = factor(rep(seq_len(10), each = 2)),
+ stringsAsFactors = FALSE
+ )
> rownames(sample_data) <- sample_data$sample_id
>
> fit_df <- data.frame(
+ feat_id = rep(colnames(mock_X), each = 2),
+ Coefficient = rep(c("(Intercept)", "groupB"), 5),
+ Estimate = rnorm(10),
+ `Pr(>|t|)` = runif(10),
+ padj = runif(10),
+ stringsAsFactors = FALSE
+ )
>
> # Mock dana object
> dana_obj <- list(
+ X = mock_X,
+ sdata = sample_data,
+ formula_rhs = ~ group,
+ fit = fit_df,
+ lrt = data.frame(), #' empty but valid
+ ranef = data.frame() #' empty but valid
+ )
> class(dana_obj) <- "dana"
>
> dana_obj <- dana_obj |>
+ ready_plots(
+ term_name = "group",
+ pval_match = "padj",
+ alpha = 0.5,
+ add_labels = FALSE,
+ plot_coeff = TRUE,
+ plot_feat = TRUE,
+ plot_ranef = FALSE,
+ sdata_var = "group",
+ verbose = FALSE
+ )
Error in `ggplot2::geom_violin()`:
! `draw_quantiles` must be a <numeric> vector, not `TRUE`.
Backtrace:
▆
1. └─readyomics::ready_plots(...)
2. └─readyomics:::plot_feat(...)
3. └─ggplot2::geom_violin(draw_quantiles = TRUE)
4. └─ggplot2:::check_numeric(draw_quantiles)
5. └─ggplot2:::check_object(x, is.numeric, what, ..., arg = arg, call = call)
6. └─ggplot2:::stop_input_type(...)
7. └─rlang::abort(message, ..., call = call, arg = arg)
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
build_phyloseq 5.519 0.451 6.375
dana 4.360 0.208 5.211
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.1.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [20s/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(readyomics)
>
> test_check("readyomics")
Error in smooth.spline(lambda, pi0, df = smooth.df) :
missing or infinite values in inputs are not allowed
2 samples found in common between 2 rows in 'X' and 2 rows in 'sample_data'.
Computing profile confidence intervals ...
refitting model(s) with ML (instead of REML)
boundary (singular) fit: see help('isSingular')
Computing profile confidence intervals ...
boundary (singular) fit: see help('isSingular')
refitting model(s) with ML (instead of REML)
boundary (singular) fit: see help('isSingular')
Computing profile confidence intervals ...
boundary (singular) fit: see help('isSingular')
refitting model(s) with ML (instead of REML)
boundary (singular) fit: see help('isSingular')
Computing profile confidence intervals ...
refitting model(s) with ML (instead of REML)
PCA
10 samples x 4 variables
standard scaling of predictors
R2X(cum) pre ort
Total 0.817 2 0
PCA
10 samples x 4 variables
standard scaling of predictors
R2X(cum) pre ort
Total 0.797 2 0
10 samples found in common between 10 rows in 'X' and 10 rows in 'sample_data'.
10 samples found in common between 10 rows in 'X' and 10 rows in 'sample_data'.
PCA
10 samples x 4 variables
standard scaling of predictors
R2X(cum) pre ort
Total 0.813 2 0
10 samples found in common between 10 rows in 'X' and 10 rows in 'sample_data'.
Permutation parameters for group have not been specified. Default 'perm_control$joint_terms' will be used.
10 samples found in common between 10 rows in 'X' and 10 rows in 'sample_data'.
Permutation parameters for group have not been specified. Default 'perm_control$joint_terms' will be used.
10 samples found in common between 10 rows in 'X' and 10 rows in 'sample_data'.
Permutation parameters for group have not been specified. Default 'perm_control$joint_terms' will be used.
2 out of 4 features were kept after 80 % prevalence filter.
4 out of 4 features were kept after 80 % prevalence filter.
4 out of 4 features were kept after 80 % prevalence filter.
[ FAIL 4 | WARN 4 | SKIP 0 | PASS 119 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-ready_plots.R:39:3'): ready_plots generates plots from a minimal dana object (fit analysis) ──
Error in `ggplot2::geom_violin(ggplot2::aes(fill = .data[[sdata_var]]),
draw_quantiles = TRUE, linewidth = 0.1, scale = "width",
show.legend = FALSE)`: `draw_quantiles` must be a <numeric> vector, not `TRUE`.
Backtrace:
▆
1. └─readyomics::ready_plots(...) at test-ready_plots.R:39:3
2. └─readyomics:::plot_feat(...)
3. └─ggplot2::geom_violin(draw_quantiles = TRUE)
4. └─ggplot2:::check_numeric(draw_quantiles)
5. └─ggplot2:::check_object(x, is.numeric, what, ..., arg = arg, call = call)
6. └─ggplot2:::stop_input_type(...)
7. └─rlang::abort(message, ..., call = call, arg = arg)
── Error ('test-ready_plots.R:163:3'): ready_plots supports paired_id if present ──
Error in `ggplot2::geom_violin(ggplot2::aes(fill = .data[[sdata_var]]),
draw_quantiles = TRUE, linewidth = 0.1, scale = "width",
show.legend = FALSE)`: `draw_quantiles` must be a <numeric> vector, not `TRUE`.
Backtrace:
▆
1. └─readyomics::ready_plots(...) at test-ready_plots.R:163:3
2. └─readyomics:::plot_feat(...)
3. └─ggplot2::geom_violin(draw_quantiles = TRUE)
4. └─ggplot2:::check_numeric(draw_quantiles)
5. └─ggplot2:::check_object(x, is.numeric, what, ..., arg = arg, call = call)
6. └─ggplot2:::stop_input_type(...)
7. └─rlang::abort(message, ..., call = call, arg = arg)
── Error ('test-ready_plots.R:205:5'): ready_plots falls back to 'feat_id' when no label columns are found ──
Error in `ggplot2::geom_violin(ggplot2::aes(fill = .data[[sdata_var]]),
draw_quantiles = TRUE, linewidth = 0.1, scale = "width",
show.legend = FALSE)`: `draw_quantiles` must be a <numeric> vector, not `TRUE`.
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-ready_plots.R:204:3
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. └─readyomics::ready_plots(...) at test-ready_plots.R:205:5
8. └─readyomics:::plot_feat(...)
9. └─ggplot2::geom_violin(draw_quantiles = TRUE)
10. └─ggplot2:::check_numeric(draw_quantiles)
11. └─ggplot2:::check_object(x, is.numeric, what, ..., arg = arg, call = call)
12. └─ggplot2:::stop_input_type(...)
13. └─rlang::abort(message, ..., call = call, arg = arg)
── Error ('test-ready_plots.R:246:3'): ready_plots respects custom X_colnames input ──
Error in `ggplot2::geom_violin(ggplot2::aes(fill = .data[[sdata_var]]),
draw_quantiles = TRUE, linewidth = 0.1, scale = "width",
show.legend = FALSE)`: `draw_quantiles` must be a <numeric> vector, not `TRUE`.
Backtrace:
▆
1. └─readyomics::ready_plots(...) at test-ready_plots.R:246:3
2. └─readyomics:::plot_feat(...)
3. └─ggplot2::geom_violin(draw_quantiles = TRUE)
4. └─ggplot2:::check_numeric(draw_quantiles)
5. └─ggplot2:::check_object(x, is.numeric, what, ..., arg = arg, call = call)
6. └─ggplot2:::stop_input_type(...)
7. └─rlang::abort(message, ..., call = call, arg = arg)
[ FAIL 4 | WARN 4 | SKIP 0 | PASS 119 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.1.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘readyomics.Rmd’ using rmarkdown
Quitting from readyomics.Rmd:412-419 [unnamed-chunk-33]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NULL
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'readyomics.Rmd' failed with diagnostics:
`draw_quantiles` must be a <numeric> vector, not `TRUE`.
--- failed re-building ‘readyomics.Rmd’
SUMMARY: processing the following file failed:
‘readyomics.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc