Last updated on 2025-01-19 05:49:17 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.1.3 | 8.24 | 176.94 | 185.18 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 2.1.3 | 4.81 | 118.13 | 122.94 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2.1.3 | 302.44 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2.1.3 | 325.38 | OK | |||
| r-devel-windows-x86_64 | 2.1.3 | 12.00 | 340.00 | 352.00 | OK | |
| r-patched-linux-x86_64 | 2.1.3 | 7.94 | 167.54 | 175.48 | OK | |
| r-release-linux-x86_64 | 2.1.3 | 6.43 | 166.19 | 172.62 | 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 | 11.00 | 300.00 | 311.00 | OK | |
| 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 | 11.00 | 382.00 | 393.00 | OK |
Version: 2.1.3
Check: examples
Result: ERROR
Running examples in ‘PubChemR-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: download
> ### Title: Download Content from PubChem and Save to a File
> ### Aliases: download
>
> ### ** Examples
>
> # Download JSON file for the compound "aspirin" into "Aspirin.JSON"
> # A folder named "Compound" will be created under current directory"
> download(
+ filename = "Aspirin",
+ outformat = "json",
+ path = "./Compound",
+ identifier = "aspirin",
+ namespace = "name",
+ domain = "compound",
+ overwrite = TRUE
+ )
Error in curl::curl_fetch_memory(url, handle = handle) :
Timeout was reached [pubchem.ncbi.nlm.nih.gov]: Resolving timed out after 10001 milliseconds
Calls: download ... request_fetch.write_memory -> <Anonymous> -> raise_libcurl_error
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
AIDs-SIDs-CIDs 0.174 0.002 145.351
Flavor: r-devel-linux-x86_64-debian-clang
Version: 2.1.3
Check: tests
Result: ERROR
Running ‘testthat.R’ [8s/188s]
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")
+ }
Error in curl::curl_fetch_memory(url, handle = handle) :
Timeout was reached [pubchem.ncbi.nlm.nih.gov]: Resolving timed out after 10000 milliseconds
The file has been saved to '/home/hornik/tmp/scratch/Rtmp2txSXR/aspirin.json'
The file has been saved to '/home/hornik/tmp/scratch/Rtmp2txSXR/aspirin.json'
The file has been saved to '/home/hornik/tmp/scratch/Rtmp2txSXR/aspirin.json'
The file has been saved to '/home/hornik/tmp/scratch/Rtmp2txSXR/aspirin.sdf'
Request failed [400]. Retrying in 1.2 seconds...
Request failed [400]. Retrying in 4.6 seconds...
SDF file saved successfully:
File Name: 'aspirin_20250116_183631.sdf'
Saved at: /home/hornik/tmp/scratch/Rtmp2txSXR
SDF file saved successfully:
File Name: 'file.sdf'
Saved at: /home/hornik/tmp/scratch/Rtmp2txSXR
'path' is not specified. Saving files into a temporary folder.
SDF file saved successfully:
File Name: 'file.sdf'
Saved at: /home/hornik/tmp/scratch/Rtmp2txSXR
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 3 | WARN 1 | SKIP 0 | PASS 198 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-00_globals.R:66:3'): succesfully returned primary class of given object ──
primaryClass(instance(tmp)) (`actual`) not equal to "PubChemInstance" (`expected`).
`actual`: "NULL"
`expected`: "PubChemInstance"
── Error ('test-00_globals.R:83:3'): slot details successfully printed ─────────
<subscriptOutOfBoundsError/error/condition>
Error in `x[[1]]`: subscript out of bounds
Backtrace:
▆
1. ├─testthat::expect_output(printSlotDetails(find_last_layer(pview$result))) at test-00_globals.R:83:3
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─testthat::capture_output_lines(code, print, width = width)
5. │ │ └─testthat:::eval_with_output(code, print = print, width = width)
6. │ │ ├─withr::with_output_sink(path, withVisible(code))
7. │ │ │ └─base::force(code)
8. │ │ └─base::withVisible(code)
9. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
10. ├─PubChemR:::printSlotDetails(find_last_layer(pview$result))
11. └─PubChemR:::find_last_layer(pview$result)
── 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)
[ FAIL 3 | WARN 1 | SKIP 0 | PASS 198 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 2.1.3
Check: for non-standard things in the check directory
Result: NOTE
Found the following files/directories:
‘Compound’
Flavor: r-devel-linux-x86_64-debian-clang