Last updated on 2025-09-29 08:49:40 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.1.5 | 8.13 | 180.09 | 188.22 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.1.5 | 5.20 | 118.51 | 123.71 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2.1.5 | 294.29 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2.1.5 | 302.82 | OK | |||
| r-devel-windows-x86_64 | 2.1.5 | 13.00 | 564.00 | 577.00 | ERROR | |
| r-patched-linux-x86_64 | 2.1.5 | 6.56 | 171.09 | 177.65 | ERROR | |
| r-release-linux-x86_64 | 2.1.5 | 8.19 | 173.32 | 181.51 | OK | |
| r-release-macos-arm64 | 2.1.5 | 247.00 | OK | |||
| r-release-macos-x86_64 | 2.1.5 | 385.00 | OK | |||
| r-release-windows-x86_64 | 2.1.5 | 10.00 | 331.00 | 341.00 | OK | |
| r-oldrel-macos-arm64 | 2.1.5 | 260.00 | NOTE | |||
| r-oldrel-macos-x86_64 | 2.1.5 | 461.00 | NOTE | |||
| r-oldrel-windows-x86_64 | 2.1.5 | 15.00 | 388.00 | 403.00 | NOTE |
Version: 2.1.5
Check: tests
Result: ERROR
Running 'testthat.R' [80s]
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_09_25_01_50_00_17305\Rtmpozki7J/aspirin.json'
The file has been saved to 'D:\temp\2025_09_25_01_50_00_17305\Rtmpozki7J/aspirin.json'
The file has been saved to 'D:\temp\2025_09_25_01_50_00_17305\Rtmpozki7J/aspirin.json'
The file has been saved to 'D:\temp\2025_09_25_01_50_00_17305\Rtmpozki7J/aspirin.json'
The file has been saved to 'D:\temp\2025_09_25_01_50_00_17305\Rtmpozki7J/aspirin.sdf'
Request failed [400]. Retrying in 1 seconds...
Request failed [400]. Retrying in 6.2 seconds...
SDF file saved successfully:
File Name: 'aspirin_20250925_081918.sdf'
Saved at: D:\temp\2025_09_25_01_50_00_17305\Rtmpozki7J
SDF file saved successfully:
File Name: 'file.sdf'
Saved at: D:\temp\2025_09_25_01_50_00_17305\Rtmpozki7J
'path' is not specified. Saving files into a temporary folder.
SDF file saved successfully:
File Name: 'file.sdf'
Saved at: D:\temp\2025_09_25_01_50_00_17305\Rtmpozki7J
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_pug_view.R:28:3'): 'annotation' cannot be NULL: Default is 'data' ──
`tmp` (`actual`) not identical to `pview2` (`expected`).
`actual$result` is length 0
`expected$result` is length 1
`names(actual$result)` is absent
`names(expected$result)` is a character vector ('Record')
`actual$result$Record` is absent
`expected$result$Record` is a list
`actual$request_args` is length 0
`expected$request_args` is length 9
`names(actual$request_args)` is absent
`names(expected$request_args)` is a character vector ('annotation', 'identifier', 'domain', 'output', 'heading', ...)
`actual$request_args$annotation` is absent
`expected$request_args$annotation` is a character vector ('data')
`actual$request_args$identifier` is absent
`expected$request_args$identifier` is a character vector ('2244')
`actual$request_args$domain` is absent
`expected$request_args$domain` is a character vector ('compound')
`actual$request_args$output` is absent
`expected$request_args$output` is a character vector ('JSON')
`actual$request_args$heading` is absent
`expected$request_args$heading` is NULL
`actual$request_args$headingType` is absent
`expected$request_args$headingType` is NULL
`actual$request_args$page` is absent
`expected$request_args$page` is NULL
`actual$request_args$qrSize` is absent
`expected$request_args$qrSize` is a character vector ('short')
`actual$request_args$save` is absent
`expected$request_args$save` is a logical vector (FALSE)
`actual$success`: FALSE
`expected$success`: TRUE
`actual$error` is a list
`expected$error` is NULL
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 169 ]
Error: Test failures
Execution halted
Flavor: r-devel-windows-x86_64
Version: 2.1.5
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-devel-windows-x86_64
Version: 2.1.5
Check: tests
Result: ERROR
Running ‘testthat.R’ [6s/94s]
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 '/home/hornik/tmp/scratch/RtmpRb0O60/aspirin.json'
The file has been saved to '/home/hornik/tmp/scratch/RtmpRb0O60/aspirin.json'
The file has been saved to '/home/hornik/tmp/scratch/RtmpRb0O60/aspirin.json'
The file has been saved to '/home/hornik/tmp/scratch/RtmpRb0O60/aspirin.json'
The file has been saved to '/home/hornik/tmp/scratch/RtmpRb0O60/aspirin.sdf'
Request failed [400]. Retrying in 2.4 seconds...
Request failed [400]. Retrying in 1 seconds...
SDF file saved successfully:
File Name: 'aspirin_20250924_072604.sdf'
Saved at: /home/hornik/tmp/scratch/RtmpRb0O60
SDF file saved successfully:
File Name: 'file.sdf'
Saved at: /home/hornik/tmp/scratch/RtmpRb0O60
'path' is not specified. Saving files into a temporary folder.
SDF file saved successfully:
File Name: 'file.sdf'
Saved at: /home/hornik/tmp/scratch/RtmpRb0O60
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 4 | WARN 9 | SKIP 0 | PASS 166 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── 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_pug_view.R:28:3'): 'annotation' cannot be NULL: Default is 'data' ──
`tmp` (`actual`) not identical to `pview2` (`expected`).
`actual$result` is length 0
`expected$result` is length 1
`names(actual$result)` is absent
`names(expected$result)` is a character vector ('Record')
`actual$result$Record` is absent
`expected$result$Record` is a list
`actual$request_args` is length 0
`expected$request_args` is length 9
`names(actual$request_args)` is absent
`names(expected$request_args)` is a character vector ('annotation', 'identifier', 'domain', 'output', 'heading', ...)
`actual$request_args$annotation` is absent
`expected$request_args$annotation` is a character vector ('data')
`actual$request_args$identifier` is absent
`expected$request_args$identifier` is a character vector ('2244')
`actual$request_args$domain` is absent
`expected$request_args$domain` is a character vector ('compound')
`actual$request_args$output` is absent
`expected$request_args$output` is a character vector ('JSON')
`actual$request_args$heading` is absent
`expected$request_args$heading` is NULL
`actual$request_args$headingType` is absent
`expected$request_args$headingType` is NULL
`actual$request_args$page` is absent
`expected$request_args$page` is NULL
`actual$request_args$qrSize` is absent
`expected$request_args$qrSize` is a character vector ('short')
`actual$request_args$save` is absent
`expected$request_args$save` is a logical vector (FALSE)
`actual$success`: FALSE
`expected$success`: TRUE
`actual$error` is a list
`expected$error` is NULL
[ FAIL 4 | WARN 9 | SKIP 0 | PASS 166 ]
Error: Test failures
Execution halted
Flavor: r-patched-linux-x86_64
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