* using log directory 'd:/RCompile/CRANincoming/R-devel/OmicFlow.Rcheck' * using R Under development (unstable) (2025-08-19 r88650 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'OmicFlow/DESCRIPTION' ... OK * this is package 'OmicFlow' version '1.3.0' * package encoding: UTF-8 * checking CRAN incoming feasibility ... NOTE Maintainer: 'Alem Gusinac ' New submission Possibly misspelled words in DESCRIPTION: Omics (2:58) omics (21:93) * 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 hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'OmicFlow' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking for future file timestamps ... 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 ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... 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 ... [15s] OK * checking Rd files ... 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 examples ... 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" + ) $plot Error in `gghalves::geom_half_point_panel()`: ! Problem while converting geom to grob. ℹ Error occurred in the 2nd layer. Caused by error in `fun()`: ! argument "layout" is missing, with no default Backtrace: ▆ 1. ├─base (local) ``(x) 2. ├─ggplot2 (local) `print.ggplot2::ggplot`(x) 3. │ ├─ggplot2::ggplot_gtable(data) 4. │ └─ggplot2 (local) `ggplot_gtable.ggplot2::ggplot_built`(data) 5. │ └─ggplot2:::by_layer(...) 6. │ ├─rlang::try_fetch(...) 7. │ │ ├─base::tryCatch(...) 8. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 9. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 10. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 11. │ │ └─base::withCallingHandlers(...) 12. │ └─ggplot2 (local) f(l = layers[[i]], d = data[[i]]) 13. │ └─l$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) ``(``) 30. └─handlers[[1L]](cnd) 31. └─cli::cli_abort(...) 32. └─rlang::abort(...) Execution halted * checking for unstated dependencies in 'tests' ... OK * checking tests ... ERROR Running 'testthat.R' 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) > > 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. └─rlang (local) ``(``) 62. └─handlers[[1L]](cnd) 63. └─cli::cli_abort(...) 64. └─rlang::abort(...) [ FAIL 1 | WARN 0 | SKIP 9 | PASS 2 ] Error: Test failures Execution halted * checking PDF version of manual ... [14s] OK * checking HTML version of manual ... OK * DONE Status: 2 ERRORs, 1 NOTE