• using R Under development (unstable) (2025-09-10 r88809)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     Debian clang version 19.1.7 (3+b2)     Debian flang-new version 19.1.7 (3+b2)
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8
• checking for file ‘readyomics/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘readyomics’ version ‘0.1.1’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [1s/2s] OK
• checking package namespace information ... OK
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking whether package ‘readyomics’ can be installed ... OK See the install log for details.
• checking package directory ... OK
• checking for future file timestamps ... OK
• checking ‘build’ directory ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
• checking for left-over files ... OK
• checking index information ... OK
• checking package subdirectories ... OK
• checking code files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... [0s/1s] OK
• checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
• checking whether the package can be unloaded cleanly ... [0s/1s] OK
• checking whether the namespace can be loaded with stated dependencies ... [0s/1s] OK
• checking whether the namespace can be unloaded cleanly ... [0s/1s] OK
• checking loading without being on the library search path ... [0s/1s] OK
• checking use of S3 registration ... OK
• checking dependencies in R code ... OK
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... [7s/9s] OK
• checking Rd files ... [0s/1s] OK
• checking Rd metadata ... OK
• checking Rd line widths ... OK
• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
• checking Rd contents ... OK
• checking for unstated dependencies in examples ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [25s/30s] 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
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [29s/34s] 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
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [58s/74s] 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
• checking PDF version of manual ... [6s/8s] OK
• checking HTML version of manual ... [1s/1s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 3 ERRORs