Last updated on 2025-06-11 05:50:24 CEST.
| Package | ERROR | OK |
|---|---|---|
| fastml | 13 | |
| genSEIR | 13 | |
| MVN | 13 | |
| PubChemR | 1 | 12 |
| rPDBapi | 1 | 12 |
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: ERROR: 1, OK: 12
Version: 2.1.4
Check: tests
Result: ERROR
Running 'testthat.R' [54s]
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\2025_06_09_01_50_00_19772\RtmpyYcz7X/aspirin.json'
The file has been saved to 'D:\temp\2025_06_09_01_50_00_19772\RtmpyYcz7X/aspirin.json'
The file has been saved to 'D:\temp\2025_06_09_01_50_00_19772\RtmpyYcz7X/aspirin.json'
The file has been saved to 'D:\temp\2025_06_09_01_50_00_19772\RtmpyYcz7X/aspirin.json'
The file has been saved to 'D:\temp\2025_06_09_01_50_00_19772\RtmpyYcz7X/aspirin.sdf'
Error in value[[3L]](cond) :
Failed to retrieve sources for the specified domain: c(Code = "PUGREST.ServerBusy", Message = "Too many requests or server too busy")
Request failed [400]. Retrying in 1 seconds...
Request failed [400]. Retrying in 1 seconds...
SDF file saved successfully:
File Name: 'aspirin_20250609_061309.sdf'
Saved at: D:\temp\2025_06_09_01_50_00_19772\RtmpyYcz7X
SDF file saved successfully:
File Name: 'file.sdf'
Saved at: D:\temp\2025_06_09_01_50_00_19772\RtmpyYcz7X
'path' is not specified. Saving files into a temporary folder.
SDF file saved successfully:
File Name: 'file.sdf'
Saved at: D:\temp\2025_06_09_01_50_00_19772\RtmpyYcz7X
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 2 | WARN 0 | SKIP 0 | PASS 168 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-get_all_sources.R:9:3'): get all sources for 'substance' ─────
inherits(tmp, "try-error") is not FALSE
`actual`: TRUE
`expected`: FALSE
── Failure ('test-get_all_sources.R:10:3'): get all sources for 'substance' ────
all(...) is not TRUE
`actual`: FALSE
`expected`: TRUE
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 168 ]
Error: Test failures
Execution halted
Flavor: r-release-windows-x86_64
Current CRAN status: ERROR: 1, OK: 12
Version: 2.1.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [35s/198s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(rPDBapi)
>
> test_check("rPDBapi")
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 70 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_get_pdb_file.R:3:3'): get_pdb_file downloads and parses the PDB file correctly ──
Error in `value[[3L]](cond)`: API Error: Failed to retrieve data for PDB ID '4HHB'. Error: HTTP Error: Request to https://files.rcsb.org/download/4HHB.pdb.gz failed with status: - Server error: (504) Gateway Timeout
Backtrace:
▆
1. └─rPDBapi::get_pdb_file("4HHB", filetype = "pdb", save = FALSE) at test_get_pdb_file.R:3:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 70 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang