Last updated on 2025-02-21 02:52:21 CET.
Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
---|---|---|---|---|---|---|
r-devel-linux-x86_64-debian-clang | 2.1.3 | 8.11 | 181.12 | 189.23 | OK | |
r-devel-linux-x86_64-debian-gcc | 2.1.3 | 5.50 | 119.44 | 124.94 | ERROR | |
r-devel-linux-x86_64-fedora-clang | 2.1.3 | 306.29 | OK | |||
r-devel-linux-x86_64-fedora-gcc | 2.1.3 | 314.40 | OK | |||
r-devel-macos-arm64 | 2.1.3 | 232.00 | OK | |||
r-devel-macos-x86_64 | 2.1.3 | 442.00 | OK | |||
r-devel-windows-x86_64 | 2.1.3 | 10.00 | 346.00 | 356.00 | OK | |
r-patched-linux-x86_64 | 2.1.3 | 8.99 | 164.63 | 173.62 | OK | |
r-release-linux-x86_64 | 2.1.3 | 7.55 | 167.15 | 174.70 | OK | |
r-release-macos-arm64 | 2.1.3 | 232.00 | OK | |||
r-release-macos-x86_64 | 2.1.3 | 311.00 | OK | |||
r-release-windows-x86_64 | 2.1.3 | 10.00 | 429.00 | 439.00 | ERROR | |
r-oldrel-macos-arm64 | 2.1.3 | 232.00 | OK | |||
r-oldrel-macos-x86_64 | 2.1.3 | 323.00 | OK | |||
r-oldrel-windows-x86_64 | 2.1.3 | 13.00 | 441.00 | 454.00 | OK |
Version: 2.1.3
Check: tests
Result: ERROR
Running ‘testthat.R’ [5s/45s]
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/Rtmph9UCRz/aspirin.json'
The file has been saved to '/tmp/Rtmph9UCRz/aspirin.json'
The file has been saved to '/tmp/Rtmph9UCRz/aspirin.json'
The file has been saved to '/tmp/Rtmph9UCRz/aspirin.json'
The file has been saved to '/tmp/Rtmph9UCRz/aspirin.sdf'
Request failed [400]. Retrying in 1.6 seconds...
Request failed [400]. Retrying in 1.1 seconds...
SDF file saved successfully:
File Name: 'aspirin_20250220_134541.sdf'
Saved at: /tmp/Rtmph9UCRz
SDF file saved successfully:
File Name: 'file.sdf'
Saved at: /tmp/Rtmph9UCRz
'path' is not specified. Saving files into a temporary folder.
SDF file saved successfully:
File Name: 'file.sdf'
Saved at: /tmp/Rtmph9UCRz
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 203 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-get_compounds.R:30:1'): pulling via 'smiles' is succesfull ───
allSuccess(object) is not TRUE
`actual`: FALSE
`expected`: TRUE
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 203 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 2.1.3
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
--- finished 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
Quitting from lines 1039-1048 [download_jsson] (Working_with_PubChemR_to_Access_Chemical_Data.Rmd)
Error: processing vignette 'Working_with_PubChemR_to_Access_Chemical_Data.Rmd' failed with diagnostics:
Timeout was reached [pubchem.ncbi.nlm.nih.gov]: Failed to connect to pubchem.ncbi.nlm.nih.gov port 443 after 10002 ms: Timeout was reached
--- failed re-building 'Working_with_PubChemR_to_Access_Chemical_Data.Rmd'
SUMMARY: processing the following file failed:
'Working_with_PubChemR_to_Access_Chemical_Data.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-release-windows-x86_64