Running 'testthat.R' [88s]
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 'D:\temp\RtmpwTLbYM/aspirin.json'
  The file has been saved to 'D:\temp\RtmpwTLbYM/aspirin.json'
  The file has been saved to 'D:\temp\RtmpwTLbYM/aspirin.json'
  The file has been saved to 'D:\temp\RtmpwTLbYM/aspirin.json'
  The file has been saved to 'D:\temp\RtmpwTLbYM/aspirin.sdf'
  Error in parse(text = command_string) : <text>:1:9: unexpected symbol
  1: Timeout was
              ^
  Error in UseMethod("retrieve") : 
    no applicable method for 'retrieve' applied to an object of class "character"
  
  trying URL 'https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/2244/SDF'
  downloaded 3641 bytes
  
  trying URL 'https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/2244/SDF'
  downloaded 3641 bytes
  
  trying URL 'https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/aspirin/SDF'
  downloaded 3641 bytes
  
    SDF file to save --> 'aspirin_2024-09-27_08_45_41.100472.sdf'
  
    Saved into folder --> D:\temp\RtmpwTLbYM
  
    Completed options
  
  trying URL 'https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/2244/SDF'
  downloaded 3641 bytes
  
    SDF file to save --> 'file.sdf'
  
    Saved into folder --> D:\temp\RtmpwTLbYM
  
    Completed options
  
  'path' is not specified. Saving files into a temporary folder.
  trying URL 'https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/aspirin/SDF'
  downloaded 3641 bytes
  
    SDF file to save --> 'file.sdf'
  
    Saved into folder --> D:\temp\RtmpwTLbYM
  
    Completed options
  
  Error in parse(text = command_string) : <text>:1:9: unexpected symbol
  1: Timeout was
              ^
  
   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 5 | WARN 1 | SKIP 0 | PASS 176 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-get_cids.R:19:3'): (code run outside of `test_that()`) ─────────
  <subscriptOutOfBoundsError/error/condition>
  Error in `object[["request_args"]]`: subscript out of bounds
  Backtrace:
      ▆
   1. └─PubChemR (local) test1(cids) at test-get_cids.R:33:1
   2.   ├─testthat::test_that(...) at test-get_cids.R:19:3
   3.   │ └─testthat:::check_string(desc)
   4.   │   └─testthat:::.rlang_check_is_string(...)
   5.   │     └─rlang::is_string(x)
   6.   ├─base::paste0(...)
   7.   └─PubChemR::request_args(object, "namespace")
  ── Failure ('test-get_compounds.R:44:3'): instance() returns an object of class 'PubChemInstance' ──
  "PubChemInstance" %in% class(instance(compounds)) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-get_compounds.R:45:3'): instance() returns an object of class 'PubChemInstance' ──
  `print\(instance\(compounds\)\)` does not match "An object of class 'PubChemInstance'".
  Actual value: "NULL"
  Backtrace:
      ▆
   1. └─testthat::expect_output(print(instance(compounds)), "An object of class 'PubChemInstance'") at test-get_compounds.R:45:3
   2.   └─testthat::expect_match(...)
   3.     └─testthat:::expect_match_(...)
  ── Error ('test-get_compounds.R:50:3'): retrieve() returns selected slots as expected for a compound ──
  Error in `UseMethod("retrieve")`: no applicable method for 'retrieve' applied to an object of class "character"
  Backtrace:
      ▆
   1. ├─testthat::expect_identical(...) at test-get_compounds.R:50:3
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. ├─PubChemR::retrieve(...)
   5. └─PubChemR:::retrieve.PubChemInstanceList(...)
   6.   ├─base::do.call("retrieve", args)
   7.   └─PubChemR::retrieve(.slot = "id", .to.data.frame = TRUE, .combine.all = FALSE)
  ── Error ('test-get_sids.R:19:3'): (code run outside of `test_that()`) ─────────
  <subscriptOutOfBoundsError/error/condition>
  Error in `object[["request_args"]]`: subscript out of bounds
  Backtrace:
      ▆
   1. └─PubChemR (local) test1(sids) at test-get_sids.R:33:1
   2.   ├─testthat::test_that(...) at test-get_sids.R:19:3
   3.   │ └─testthat:::check_string(desc)
   4.   │   └─testthat:::.rlang_check_is_string(...)
   5.   │     └─rlang::is_string(x)
   6.   ├─base::paste0(...)
   7.   └─PubChemR::request_args(object, "namespace")
  
  [ FAIL 5 | WARN 1 | SKIP 0 | PASS 176 ]
  Error: Test failures
  Execution halted