Last updated on 2025-09-16 12:52:40 CEST.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| fastml | 13 | ||
| genSEIR | 13 | ||
| MVN | 13 | ||
| PubChemR | 1 | 3 | 9 |
| rPDBapi | 13 |
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: ERROR: 1, NOTE: 3, OK: 9
Version: 2.1.5
Check: tests
Result: ERROR
Running ‘testthat.R’ [5s/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/RtmphzoetS/aspirin.json'
The file has been saved to '/tmp/RtmphzoetS/aspirin.json'
The file has been saved to '/tmp/RtmphzoetS/aspirin.json'
The file has been saved to '/tmp/RtmphzoetS/aspirin.json'
The file has been saved to '/tmp/RtmphzoetS/aspirin.sdf'
Request failed [400]. Retrying in 2.2 seconds...
Request failed [400]. Retrying in 3.6 seconds...
SDF file saved successfully:
File Name: 'aspirin_20250915_135725.sdf'
Saved at: /tmp/RtmphzoetS
SDF file saved successfully:
File Name: 'file.sdf'
Saved at: /tmp/RtmphzoetS
'path' is not specified. Saving files into a temporary folder.
SDF file saved successfully:
File Name: 'file.sdf'
Saved at: /tmp/RtmphzoetS
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 10 | SKIP 0 | PASS 163 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-00_globals.R:90:3'): section details successfully printed ──────
Error in `UseMethod("section")`: no applicable method for 'section' applied to an object of class "NULL"
Backtrace:
▆
1. ├─PubChemR::section(pview, "S1") at test-00_globals.R:90:3
2. └─PubChemR:::section.PugViewInstance(pview, "S1")
3. ├─base::do.call("section", call_args)
4. └─PubChemR::section(object = NULL, .id = "S1", .verbose = FALSE)
── Failure ('test-get_assays.R:5:1'): pulling via 'aid' is succesfull ──────────
allSuccess(object) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_assays.R:42:3'): retrieve() returns selected slots as expected for an assay ──
{
...
} is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_assays.R:61:3'): checking the effect of '.verbose' argument in retrieve() function ──
`retrieve(assay, .slot = "comment", .verbose = TRUE)` produced no output
── Failure ('test-get_synonyms.R:6:1'): pulling via 'name' is succesfull ───────
allSuccess(object) is not TRUE
`actual`: FALSE
`expected`: TRUE
[ FAIL 5 | WARN 10 | SKIP 0 | PASS 163 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 2.1.5
Check: installed package size
Result: NOTE
installed size is 5.0Mb
sub-directories of 1Mb or more:
doc 4.7Mb
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Current CRAN status: OK: 13