- using R Under development (unstable) (2025-09-24 r88873 ucrt)
- using platform: x86_64-w64-mingw32
- R was compiled by
gcc.exe (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
- running under: Windows Server 2022 x64 (build 20348)
- using session charset: UTF-8
- checking for file 'PubChemR/DESCRIPTION' ... OK
- checking extension type ... Package
- this is package 'PubChemR' version '2.1.5'
- package encoding: UTF-8
- checking package namespace information ... OK
- checking package dependencies ... OK
- checking if this is a source package ... OK
- checking if there is a namespace ... OK
- checking for hidden files and directories ... OK
- checking for portable file names ... OK
- checking whether package 'PubChemR' can be installed ... OK
See the install log for details.
- checking installed package size ... INFO
installed size is 5.0Mb
sub-directories of 1Mb or more:
doc 4.7Mb
- checking package directory ... OK
- checking 'build' directory ... OK
- checking DESCRIPTION meta-information ... OK
- checking top-level files ... OK
- checking for left-over files ... OK
- checking index information ... OK
- checking package subdirectories ... OK
- checking code files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- checking whether the package can be loaded ... [1s] OK
- checking whether the package can be loaded with stated dependencies ... [1s] OK
- checking whether the package can be unloaded cleanly ... [1s] OK
- checking whether the namespace can be loaded with stated dependencies ... [1s] OK
- checking whether the namespace can be unloaded cleanly ... [2s] OK
- checking loading without being on the library search path ... [2s] OK
- checking use of S3 registration ... OK
- checking dependencies in R code ... OK
- checking S3 generic/method consistency ... OK
- checking replacement functions ... OK
- checking foreign function calls ... OK
- checking R code for possible problems ... [7s] OK
- checking Rd files ... [1s] OK
- checking Rd metadata ... OK
- checking Rd cross-references ... OK
- checking for missing documentation entries ... OK
- checking for code/documentation mismatches ... OK
- checking Rd \usage sections ... OK
- checking Rd contents ... OK
- checking for unstated dependencies in examples ... OK
- checking installed files from 'inst/doc' ... OK
- checking files in 'vignettes' ... OK
- checking examples ... [43s] OK
- checking for unstated dependencies in 'tests' ... OK
- checking tests ... [80s] 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
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [368s] 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
- checking PDF version of manual ... [22s] OK
- checking HTML version of manual ... [5s] OK
- DONE
Status: 2 ERRORs