* using log directory ‘/data/gannet/ripley/R/packages/tests-Suggests/romic.Rcheck’ * using R Under development (unstable) (2024-08-23 r87043) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc-14 (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: Fedora Linux 36 (Workstation Edition) * using session charset: UTF-8 * using option ‘--no-stop-on-test-error’ * checking for file ‘romic/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘romic’ version ‘1.1.3’ * package encoding: UTF-8 * 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 ‘romic’ can be installed ... [15s/22s] OK * checking package directory ... 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 ... 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 ... [21s/30s] OK * checking Rd files ... NOTE checkRd: (-1) update_tidy_omic.Rd:16-17: Lost braces 16 | in \code{updated_tidy_data} (names) and the table {features, samples, | ^ * 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘romic-Ex.R’ failed The error most likely occurred in: > ### Name: impute_missing_values > ### Title: Impute Missing Values > ### Aliases: impute_missing_values > > ### ** Examples > > impute_missing_values(brauer_2008_triple) Error in impute_missing_values(brauer_2008_triple) : Install "impute" using remotes::install_bioc("impute") to use this function Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ [14s/20s] [15s/21s] ERROR 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 > > suppressPackageStartupMessages(library(testthat)) > library(romic) > > test_check("romic") [ FAIL 1 | WARN 0 | SKIP 7 | PASS 66 ] ══ Skipped tests (7) ═══════════════════════════════════════════════════════════ • On CRAN (7): 'test-data_classes.R:22:3', 'test-data_classes.R:73:3', 'test-data_classes.R:157:3', 'test-design.R:2:3', 'test-filters.R:3:3', 'test-mutates.R:32:3', 'test-mutates.R:39:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-app_heatmap.R:34:3'): Create heatmap ─────────────────────────── Error in `loadNamespace(x)`: there is no package called 'plotly' Backtrace: ▆ 1. ├─romic::plot_heatmap(...) at test-app_heatmap.R:34:3 2. │ ├─base::suppressWarnings(plotly::ggplotly(heatmap_plot) %>% plotly::layout(margin = 0)) 3. │ │ └─base::withCallingHandlers(...) 4. │ └─plotly::ggplotly(heatmap_plot) %>% plotly::layout(margin = 0) 5. └─base::loadNamespace(x) 6. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL) 7. └─base (local) withOneRestart(expr, restarts[[1L]]) 8. └─base (local) doWithOneRestart(return(expr), restart) [ FAIL 1 | WARN 0 | SKIP 7 | PASS 66 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * checking HTML version of manual ... OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 2 ERRORs, 1 NOTE See ‘/data/gannet/ripley/R/packages/tests-Suggests/romic.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 2:54.72, 109.25 + 13.90