Running ‘testthat.R’ [4s/134s]
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(PubChemR)
  > 
  > # Functions used globally in package tests (testthat) ----
  > allSuccess <- function(object){
  +   all(unlist(lapply(object$result, "[[", "success")))
  + }
  > 
  > testRequest <- function(object, ...){
  +   test_that(paste0("pulling via '", request_args(object, "namespace"), "' is succesfull"), {
  +     expect_true(allSuccess(object))
  +   })
  + 
  +   test_that("prints output to the R Console", {
  +     expect_output(print(object))
  +   })
  + }
  > 
  > # Set 'skipTests' FALSE to run test codes. This is set TRUE to skip
  > # all tests on GitHub actions since some of PubChem requests were incomplete due to
  > # timeout and/or API related issues. BUILD & CHECK actions on GitHub returns error
  > # even if all tests were passed on local installations of R.
  > skipTests <- FALSE
  > 
  > if (!skipTests){
  +   test_check("PubChemR")
  + }
  The file has been saved to '/tmp/Rtmp3lasxs/aspirin.json'
  The file has been saved to '/tmp/Rtmp3lasxs/aspirin.json'
  The file has been saved to '/tmp/Rtmp3lasxs/aspirin.json'
  The file has been saved to '/tmp/Rtmp3lasxs/aspirin.json'
  The file has been saved to '/tmp/Rtmp3lasxs/aspirin.sdf'
  
  Request failed [400]. Retrying in 3.2 seconds...
  Request failed [400]. Retrying in 7.4 seconds...
  SDF file saved successfully:
    File Name: 'aspirin_20250924_135520.sdf'
    Saved at: /tmp/Rtmp3lasxs
  SDF file saved successfully:
    File Name: 'file.sdf'
    Saved at: /tmp/Rtmp3lasxs
  'path' is not specified. Saving files into a temporary folder.
  SDF file saved successfully:
    File Name: 'file.sdf'
    Saved at: /tmp/Rtmp3lasxs
  
   PubChem Substance Details (comment)
  
   Same as: <a href="http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid=7847177">D00109</a>
   Is a reactant of enzyme EC: 3.1.1.55
  
  
   PubChem Substance Details (comment)
  
   Same as: <a href="http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid=7847177">D00109</a>
   Is a reactant of enzyme EC: 3.1.1.55
  
  [ FAIL 6 | WARN 4 | SKIP 0 | PASS 156 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-get_pug_view.R:28:3'): 'annotation' cannot be NULL: Default is 'data' ──
  `tmp` (`actual`) not identical to `pview2` (`expected`).
  
  `actual$result` is length 1
  `expected$result` is length 0
  
  `names(actual$result)` is a character vector ('Record')
  `names(expected$result)` is absent
  
  `actual$result$Record` is a list
  `expected$result$Record` is absent
  
  `actual$request_args` is length 9
  `expected$request_args` is length 0
  
  `names(actual$request_args)` is a character vector ('annotation', 'identifier', 'domain', 'output', 'heading', ...)
  `names(expected$request_args)` is absent
  
  `actual$request_args$annotation` is a character vector ('data')
  `expected$request_args$annotation` is absent
  
  `actual$request_args$identifier` is a character vector ('2244')
  `expected$request_args$identifier` is absent
  
  `actual$request_args$domain` is a character vector ('compound')
  `expected$request_args$domain` is absent
  
  `actual$request_args$output` is a character vector ('JSON')
  `expected$request_args$output` is absent
  
  `actual$request_args$heading` is NULL
  `expected$request_args$heading` is absent
  
  `actual$request_args$headingType` is NULL
  `expected$request_args$headingType` is absent
  
  `actual$request_args$page` is NULL
  `expected$request_args$page` is absent
  
  `actual$request_args$qrSize` is a character vector ('short')
  `expected$request_args$qrSize` is absent
  
  `actual$request_args$save` is a logical vector (FALSE)
  `expected$request_args$save` is absent
  
  `actual$success`:   TRUE 
  `expected$success`: FALSE
  
  `actual$error` is NULL
  `expected$error` is a list
  ── Error ('test-get_pug_view.R:36:3'): sectionList() returns a tibble with number of rows equal to the number of setions ──
  Error in `UseMethod("sectionList")`: no applicable method for 'sectionList' applied to an object of class "NULL"
  Backtrace:
      ▆
   1. ├─PubChemR::sectionList(pview2) at test-get_pug_view.R:36:3
   2. └─PubChemR:::sectionList.PugViewInstance(pview2)
   3.   ├─base::do.call("sectionList", call_args)
   4.   └─PubChemR::sectionList(object = NULL)
  ── Error ('test-get_pug_view.R:44:5'): extracting specific section lists form complete list. ──
  Error in `UseMethod("sectionList")`: no applicable method for 'sectionList' applied to an object of class "NULL"
  Backtrace:
      ▆
   1. ├─testthat::expect_true(...) at test-get_pug_view.R:43:3
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. ├─PubChemR::sectionList(...) at test-get_pug_view.R:44:5
   5. └─PubChemR:::sectionList.PugViewInstance(...)
   6.   ├─base::do.call("sectionList", call_args)
   7.   └─PubChemR::sectionList(object = NULL, .pattern = `<chr>`, .match_type = "contain")
  ── Error ('test-get_pug_view.R:54:3'): a series of tests on sectionList() ──────
  Error in `UseMethod("section")`: no applicable method for 'section' applied to an object of class "NULL"
  Backtrace:
      ▆
   1. ├─PubChemR::section(pview2) at test-get_pug_view.R:54:3
   2. └─PubChemR:::section.PugViewInstance(pview2)
   3.   ├─base::do.call("section", call_args)
   4.   └─PubChemR::section(object = NULL, .id = "S1", .verbose = FALSE)
  ── Error ('test-get_pug_view.R:73:3'): print sections in a nested way ──────────
  Error in `UseMethod("section")`: no applicable method for 'section' applied to an object of class "NULL"
  Backtrace:
       ▆
    1. ├─testthat::expect_output(...) at test-get_pug_view.R:73:3
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ └─testthat::capture_output_lines(code, print, width = width)
    5. │   │   └─testthat:::eval_with_output(code, print = print, width = width)
    6. │   │     ├─withr::with_output_sink(path, withVisible(code))
    7. │   │     │ └─base::force(code)
    8. │   │     └─base::withVisible(code)
    9. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   10. ├─PubChemR::section(section(pview2, .verbose = TRUE), .verbose = TRUE)
   11. ├─PubChemR::section(pview2, .verbose = TRUE)
   12. └─PubChemR:::section.PugViewInstance(pview2, .verbose = TRUE)
   13.   ├─base::do.call("section", call_args)
   14.   └─PubChemR::section(object = NULL, .id = "S1", .verbose = TRUE)
  ── Failure ('test-get_synonyms.R:6:1'): pulling via 'name' is succesfull ───────
  allSuccess(object) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 6 | WARN 4 | SKIP 0 | PASS 156 ]
  Error: Test failures
  Execution halted