CRAN Package Check Results for Package PubChemR

Last updated on 2025-02-21 02:52:21 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2.1.3 8.11 181.12 189.23 OK
r-devel-linux-x86_64-debian-gcc 2.1.3 5.50 119.44 124.94 ERROR
r-devel-linux-x86_64-fedora-clang 2.1.3 306.29 OK
r-devel-linux-x86_64-fedora-gcc 2.1.3 314.40 OK
r-devel-macos-arm64 2.1.3 232.00 OK
r-devel-macos-x86_64 2.1.3 442.00 OK
r-devel-windows-x86_64 2.1.3 10.00 346.00 356.00 OK
r-patched-linux-x86_64 2.1.3 8.99 164.63 173.62 OK
r-release-linux-x86_64 2.1.3 7.55 167.15 174.70 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 10.00 429.00 439.00 ERROR
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 13.00 441.00 454.00 OK

Additional issues

OpenBLAS

Check Details

Version: 2.1.3
Check: tests
Result: ERROR Running ‘testthat.R’ [5s/45s] 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/Rtmph9UCRz/aspirin.json' The file has been saved to '/tmp/Rtmph9UCRz/aspirin.json' The file has been saved to '/tmp/Rtmph9UCRz/aspirin.json' The file has been saved to '/tmp/Rtmph9UCRz/aspirin.json' The file has been saved to '/tmp/Rtmph9UCRz/aspirin.sdf' Request failed [400]. Retrying in 1.6 seconds... Request failed [400]. Retrying in 1.1 seconds... SDF file saved successfully: File Name: 'aspirin_20250220_134541.sdf' Saved at: /tmp/Rtmph9UCRz SDF file saved successfully: File Name: 'file.sdf' Saved at: /tmp/Rtmph9UCRz 'path' is not specified. Saving files into a temporary folder. SDF file saved successfully: File Name: 'file.sdf' Saved at: /tmp/Rtmph9UCRz 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 203 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-get_compounds.R:30:1'): pulling via 'smiles' is succesfull ─── allSuccess(object) is not TRUE `actual`: FALSE `expected`: TRUE [ FAIL 1 | WARN 0 | SKIP 0 | PASS 203 ] Error: Test failures Execution halted Flavor: r-devel-linux-x86_64-debian-gcc

Version: 2.1.3
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 --- finished 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 Quitting from lines 1039-1048 [download_jsson] (Working_with_PubChemR_to_Access_Chemical_Data.Rmd) Error: processing vignette 'Working_with_PubChemR_to_Access_Chemical_Data.Rmd' failed with diagnostics: Timeout was reached [pubchem.ncbi.nlm.nih.gov]: Failed to connect to pubchem.ncbi.nlm.nih.gov port 443 after 10002 ms: Timeout was reached --- failed re-building 'Working_with_PubChemR_to_Access_Chemical_Data.Rmd' SUMMARY: processing the following file failed: 'Working_with_PubChemR_to_Access_Chemical_Data.Rmd' Error: Vignette re-building failed. Execution halted Flavor: r-release-windows-x86_64