* using log directory ‘/data/gannet/ripley/R/packages/tests-Suggests/romic.Rcheck’
* using R Under development (unstable) (2024-04-19 r86451)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-13 (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* 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 ... [17s/19s] 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 ... [23s/26s] 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’ [15s/23s]
 [15s/24s] 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 ───────────────────────────
  <packageNotFoundError/error/condition>
  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 ... [10s/14s] 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 2:52.15, 124.53 + 14.61