CRAN Package Check Results for Package readyomics

Last updated on 2025-09-12 13:48:40 CEST.

Flavor	Version	Tinstall	Tcheck	Ttotal	Status	Flags
r-devel-linux-x86_64-debian-clang	0.1.1	3.39	171.91	175.30	ERROR
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

Check Details

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 8.372 0.607 10.582 dana 7.011 0.168 8.859 mva 6.212 0.211 8.141 Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.1.1
Check: tests
Result: ERROR Running ‘testthat.R’ [29s/34s] 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-clang

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 Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

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