dependentsimr

re-building of vignette outputs

Error(s) in re-building vignettes:
  ...
--- re-building ‘simulate_data.Rmd’ using rmarkdown

Quitting from simulate_data.Rmd:85-87 [unnamed-chunk-7]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlib_error_package_not_found>
Error in `fit_deseq()`:
! The package "DESeq2" is required Using type='DESeq2' requires DESeq2
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'simulate_data.Rmd' failed with diagnostics:
The package "DESeq2" is required Using type='DESeq2' requires DESeq2
--- failed re-building ‘simulate_data.Rmd’

SUMMARY: processing the following file failed:
  ‘simulate_data.Rmd’

Error: Vignette re-building failed.
Execution halted

tests

  Running ‘testthat.R’ [1s/2s]
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(dependentsimr)
  > 
  > test_check("dependentsimr")
  Saving _problems/test-dependentsim-77.R
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 6 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-dependentsim.R:77:1'): (code run outside of `test_that()`) ─────
  <rlib_error_package_not_found/rlang_error/error/condition>
  Error in `fit_deseq(data)`: The package "DESeq2" is required Using type='DESeq2' requires DESeq2
  Backtrace:
      ▆
   1. └─dependentsimr::get_random_structure(...) at test-dependentsim.R:77:1
   2.   └─dependentsimr:::marginals_and_transform(datasets, types)
   3.     └─dependentsimr:::fit_deseq(data)
   4.       └─rlang::check_installed("DESeq2", reason = "Using type='DESeq2' requires DESeq2")
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 6 ]
  Error:
  ! Test failures.
  Execution halted

*

*

*

*

*

*

*

*

*

*

*

*

*