* using log directory 'd:/Rcompile/CRANpkg/local/4.4/PubChemR.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.3.0
GNU Fortran (GCC) 13.3.0
* 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 '2.1.3'
* 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 'https://www.r-project.org/nosvn/R.check/r-release-windows-x86_64/PubChemR-00install.html' for details.
* checking installed package size ... OK
* 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 ... [1s] 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 ... [18s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [44s] ERROR
Running 'testthat.R' [44s]
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_02_25_01_50_00_15700\RtmpmWL1pM/aspirin.json'
The file has been saved to 'D:\temp\2025_02_25_01_50_00_15700\RtmpmWL1pM/aspirin.json'
The file has been saved to 'D:\temp\2025_02_25_01_50_00_15700\RtmpmWL1pM/aspirin.json'
The file has been saved to 'D:\temp\2025_02_25_01_50_00_15700\RtmpmWL1pM/aspirin.json'
The file has been saved to 'D:\temp\2025_02_25_01_50_00_15700\RtmpmWL1pM/aspirin.sdf'
Request failed [400]. Retrying in 1.3 seconds...
Request failed [400]. Retrying in 3.1 seconds...
SDF file saved successfully:
File Name: 'aspirin_20250225_103404.sdf'
Saved at: D:\temp\2025_02_25_01_50_00_15700\RtmpmWL1pM
SDF file saved successfully:
File Name: 'file.sdf'
Saved at: D:\temp\2025_02_25_01_50_00_15700\RtmpmWL1pM
'path' is not specified. Saving files into a temporary folder.
SDF file saved successfully:
File Name: 'file.sdf'
Saved at: D:\temp\2025_02_25_01_50_00_15700\RtmpmWL1pM
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 6 | WARN 0 | SKIP 0 | PASS 198 ]
â•â• Failed tests â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•
── Failure ('test-get_aids.R:20:5'): pulling aids via 'cid' is succesfull ──────
allSuccess(object) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_aids.R:24:5'): AIDs succesfully returns 'data.frame' and 'list' ──
{
...
} is not TRUE
`actual`: FALSE
`expected`: TRUE
Backtrace:
â–†
1. └─PubChemR (local) toDataFrame(object) at test-get_aids.R:24:5
2. └─testthat::expect_true(...) at test-get_aids.R:5:3
── Failure ('test-get_substances.R:6:1'): pulling via 'name' is succesfull ─────
allSuccess(object) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_substances.R:30:3'): incorrect/undefined substance identifier returns error ──
all(!is.null(tmp$result[[1]]$error), is.list(tmp$result[[1]]$error)) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_synonyms.R:6:1'): pulling via 'name' is succesfull ───────
allSuccess(object) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-get_synonyms.R:50:3'): pulling synonyms via 'cid' is succesful ──
allSuccess(tmp) is not TRUE
`actual`: FALSE
`expected`: TRUE
[ FAIL 6 | WARN 0 | SKIP 0 | PASS 198 ]
Error: Test failures
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [191s] OK
* checking PDF version of manual ... [28s] OK
* checking HTML version of manual ... [5s] OK
* DONE
Status: 1 ERROR