Last updated on 2025-08-26 01:49:29 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.1.4 | 7.64 | 179.88 | 187.52 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.1.4 | 5.46 | 76.03 | 81.49 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 2.1.4 | 295.16 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2.1.4 | 301.53 | OK | |||
| r-devel-windows-x86_64 | 2.1.4 | 11.00 | 334.00 | 345.00 | OK | |
| r-patched-linux-x86_64 | 2.1.4 | 7.74 | 172.35 | 180.09 | OK | |
| r-release-linux-x86_64 | 2.1.4 | 7.23 | 168.31 | 175.54 | OK | |
| r-release-macos-arm64 | 2.1.4 | 326.00 | OK | |||
| r-release-macos-x86_64 | 2.1.4 | 283.00 | OK | |||
| r-release-windows-x86_64 | 2.1.4 | 11.00 | 369.00 | 380.00 | OK | |
| r-oldrel-macos-arm64 | 2.1.4 | 221.00 | OK | |||
| r-oldrel-macos-x86_64 | 2.1.4 | 312.00 | OK | |||
| r-oldrel-windows-x86_64 | 2.1.4 | 14.00 | 317.00 | 331.00 | ERROR |
Version: 2.1.4
Check: tests
Result: ERROR
Running ‘testthat.R’ [5s/133s]
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/RtmpHk8hAH/aspirin.json'
The file has been saved to '/tmp/RtmpHk8hAH/aspirin.json'
The file has been saved to '/tmp/RtmpHk8hAH/aspirin.json'
The file has been saved to '/tmp/RtmpHk8hAH/aspirin.json'
The file has been saved to '/tmp/RtmpHk8hAH/aspirin.sdf'
Request failed [400]. Retrying in 1.8 seconds...
Request failed [400]. Retrying in 7.9 seconds...
Request failed [504]. Retrying in 1.8 seconds...
SDF file saved successfully:
File Name: 'aspirin_20250825_135508.sdf'
Saved at: /tmp/RtmpHk8hAH
SDF file saved successfully:
File Name: 'file.sdf'
Saved at: /tmp/RtmpHk8hAH
'path' is not specified. Saving files into a temporary folder.
SDF file saved successfully:
File Name: 'file.sdf'
Saved at: /tmp/RtmpHk8hAH
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 1 | WARN 0 | SKIP 0 | PASS 169 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-get_substances.R:6:1'): pulling via 'name' is succesfull ─────
allSuccess(object) is not TRUE
`actual`: FALSE
`expected`: TRUE
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 169 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 2.1.4
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building 'Enhancing_Chemical_Data_Access_with_PubChemR.Rmd' using rmarkdown
Quitting from Enhancing_Chemical_Data_Access_with_PubChemR.Rmd:253-255 [unnamed-chunk-26]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `UseMethod()`:
! no applicable method for 'sectionList' applied to an object of class "NULL"
---
Backtrace:
▆
1. ├─PubChemR::sectionList(object = result)
2. └─PubChemR:::sectionList.PugViewInstance(object = result)
3. ├─base::do.call("sectionList", call_args)
4. └─PubChemR::sectionList(object = NULL)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Enhancing_Chemical_Data_Access_with_PubChemR.Rmd' failed with diagnostics:
no applicable method for 'sectionList' applied to an object of class "NULL"
--- failed re-building 'Enhancing_Chemical_Data_Access_with_PubChemR.Rmd'
--- re-building 'Exploring_Chemical_Data_with_PubChemR.Rmd' using rmarkdown
--- finished re-building 'Exploring_Chemical_Data_with_PubChemR.Rmd'
--- re-building 'Working_with_PubChemR_to_Access_Chemical_Data.Rmd' using rmarkdown
--- finished re-building 'Working_with_PubChemR_to_Access_Chemical_Data.Rmd'
SUMMARY: processing the following file failed:
'Enhancing_Chemical_Data_Access_with_PubChemR.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-oldrel-windows-x86_64