CRAN Package Check Results for Package PubChemR

Last updated on 2025-04-24 14:49:40 CEST.

Flavor	Version	T_install	T_check	T_total	Status
r-devel-linux-x86_64-debian-clang	2.1.4	8.82	178.01	186.83	OK
r-devel-linux-x86_64-debian-gcc	2.1.4	5.43	115.58	121.01	ERROR
r-devel-linux-x86_64-fedora-clang	2.1.4			295.12	OK
r-devel-linux-x86_64-fedora-gcc	2.1.4			294.17	OK
r-devel-windows-x86_64	2.1.4	12.00	348.00	360.00	ERROR
r-patched-linux-x86_64	2.1.4	9.44	171.27	180.71	OK
r-release-linux-x86_64	2.1.4	8.01	169.53	177.54	OK
r-release-macos-arm64	2.1.4			326.00	OK
r-release-macos-x86_64	2.1.4			283.00	OK
r-release-windows-x86_64	2.1.4	10.00	329.00	339.00	OK
r-oldrel-macos-arm64	2.1.4			221.00	OK
r-oldrel-macos-x86_64	2.1.4			312.00	OK
r-oldrel-windows-x86_64	2.1.4	14.00	459.00	473.00	OK

Check Details

Version: 2.1.4
Check: tests
Result: ERROR Running ‘testthat.R’ [4s/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/Rtmpzg7S1m/aspirin.json' The file has been saved to '/tmp/Rtmpzg7S1m/aspirin.json' The file has been saved to '/tmp/Rtmpzg7S1m/aspirin.json' The file has been saved to '/tmp/Rtmpzg7S1m/aspirin.json' The file has been saved to '/tmp/Rtmpzg7S1m/aspirin.sdf' Error in value[[3L]](cond) : Failed to retrieve sources for the specified domain: c(Code = "PUGREST.ServerBusy", Message = "Too many requests or server too busy") Request failed [400]. Retrying in 1 seconds... Request failed [400]. Retrying in 4.1 seconds... SDF file saved successfully: File Name: 'aspirin_20250423_135207.sdf' Saved at: /tmp/Rtmpzg7S1m SDF file saved successfully: File Name: 'file.sdf' Saved at: /tmp/Rtmpzg7S1m 'path' is not specified. Saving files into a temporary folder. SDF file saved successfully: File Name: 'file.sdf' Saved at: /tmp/Rtmpzg7S1m 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 2 | WARN 0 | SKIP 0 | PASS 168 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-get_all_sources.R:9:3'): get all sources for 'substance' ───── inherits(tmp, "try-error") is not FALSE `actual`: TRUE `expected`: FALSE ── Failure ('test-get_all_sources.R:10:3'): get all sources for 'substance' ──── all(...) is not TRUE `actual`: FALSE `expected`: TRUE [ FAIL 2 | WARN 0 | SKIP 0 | PASS 168 ] Error: Test failures Execution halted Flavor: r-devel-linux-x86_64-debian-gcc

Version: 2.1.4
Check: tests
Result: ERROR Running 'testthat.R' [60s] 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_04_20_01_50_00_2710\RtmpGAqGYJ/aspirin.json' The file has been saved to 'D:\temp\2025_04_20_01_50_00_2710\RtmpGAqGYJ/aspirin.json' The file has been saved to 'D:\temp\2025_04_20_01_50_00_2710\RtmpGAqGYJ/aspirin.json' The file has been saved to 'D:\temp\2025_04_20_01_50_00_2710\RtmpGAqGYJ/aspirin.json' The file has been saved to 'D:\temp\2025_04_20_01_50_00_2710\RtmpGAqGYJ/aspirin.sdf' Request failed [400]. Retrying in 1 seconds... Request failed [400]. Retrying in 7.9 seconds... SDF file saved successfully: File Name: 'aspirin_20250420_085647.sdf' Saved at: D:\temp\2025_04_20_01_50_00_2710\RtmpGAqGYJ SDF file saved successfully: File Name: 'file.sdf' Saved at: D:\temp\2025_04_20_01_50_00_2710\RtmpGAqGYJ 'path' is not specified. Saving files into a temporary folder. SDF file saved successfully: File Name: 'file.sdf' Saved at: D:\temp\2025_04_20_01_50_00_2710\RtmpGAqGYJ 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_cids.R:20:5'): pulling cids via 'smiles' is succesfull ─── allSuccess(object) is not TRUE `actual`: FALSE `expected`: TRUE [ FAIL 1 | WARN 0 | SKIP 0 | PASS 169 ] Error: Test failures Execution halted Flavor: r-devel-windows-x86_64