CRAN Package Check Results for Package PubChemR

Last updated on 2025-08-30 18:48:40 CEST.

Flavor	Version	T_install	T_check	T_total	Status
r-devel-linux-x86_64-debian-clang	2.1.4	7.09	98.99	106.08	OK
r-devel-linux-x86_64-debian-gcc	2.1.4	5.71	120.67	126.38	ERROR
r-devel-linux-x86_64-fedora-clang	2.1.5			247.20	OK
r-devel-linux-x86_64-fedora-gcc	2.1.5			144.25	OK
r-devel-windows-x86_64	2.1.4	9.00	488.00	497.00	ERROR
r-patched-linux-x86_64	2.1.4	7.77	92.91	100.68	OK
r-release-linux-x86_64	2.1.4	7.23	168.31	175.54	OK
r-release-macos-arm64	2.1.4			326.00	OK
r-release-macos-x86_64	2.1.5			385.00	OK
r-release-windows-x86_64	2.1.4	11.00	369.00	380.00	OK
r-oldrel-macos-arm64	2.1.4			221.00	OK
r-oldrel-macos-x86_64	2.1.5			461.00	NOTE
r-oldrel-windows-x86_64	2.1.4	14.00	372.00	386.00	OK

Check Details

Version: 2.1.4
Check: tests
Result: ERROR Running ‘testthat.R’ [5s/91s] 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/Rtmpi8TGyX/aspirin.json' The file has been saved to '/tmp/Rtmpi8TGyX/aspirin.json' The file has been saved to '/tmp/Rtmpi8TGyX/aspirin.json' The file has been saved to '/tmp/Rtmpi8TGyX/aspirin.json' The file has been saved to '/tmp/Rtmpi8TGyX/aspirin.sdf' Error in value[[3L]](cond) : Failed to retrieve sources for the specified domain: c(Code = "PUGREST.Timeout", Message = "Request timed out") Request failed [400]. Retrying in 1 seconds... Request failed [400]. Retrying in 2 seconds... SDF file saved successfully: File Name: 'aspirin_20250829_135757.sdf' Saved at: /tmp/Rtmpi8TGyX SDF file saved successfully: File Name: 'file.sdf' Saved at: /tmp/Rtmpi8TGyX 'path' is not specified. Saving files into a temporary folder. SDF file saved successfully: File Name: 'file.sdf' Saved at: /tmp/Rtmpi8TGyX 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:20:3'): get all sources for 'assay' ──────── inherits(tmp, "try-error") is not FALSE `actual`: TRUE `expected`: FALSE ── Failure ('test-get_all_sources.R:21:3'): get all sources for 'assay' ──────── 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' [85s] 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_08_29_01_50_00_1538\RtmpkJz7Ez/aspirin.json' The file has been saved to 'D:\temp\2025_08_29_01_50_00_1538\RtmpkJz7Ez/aspirin.json' The file has been saved to 'D:\temp\2025_08_29_01_50_00_1538\RtmpkJz7Ez/aspirin.json' The file has been saved to 'D:\temp\2025_08_29_01_50_00_1538\RtmpkJz7Ez/aspirin.json' The file has been saved to 'D:\temp\2025_08_29_01_50_00_1538\RtmpkJz7Ez/aspirin.sdf' Request failed [400]. Retrying in 2.6 seconds... Request failed [400]. Retrying in 2.7 seconds... SDF file saved successfully: File Name: 'aspirin_20250829_090915.sdf' Saved at: D:\temp\2025_08_29_01_50_00_1538\RtmpkJz7Ez SDF file saved successfully: File Name: 'file.sdf' Saved at: D:\temp\2025_08_29_01_50_00_1538\RtmpkJz7Ez 'path' is not specified. Saving files into a temporary folder. SDF file saved successfully: File Name: 'file.sdf' Saved at: D:\temp\2025_08_29_01_50_00_1538\RtmpkJz7Ez [ FAIL 4 | WARN 7 | SKIP 0 | PASS 166 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── 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:35:3'): '.verbose' works as expected ──────── retrieve(...) returns visibly, not invisibly. ── Failure ('test-get_substances.R:38:3'): '.verbose' works as expected ──────── retrieve(...) returns visibly, not invisibly. ── Failure ('test-get_substances.R:50:3'): return error for unavailable substance idx. ── `retrieve(tmp, .slot = "comment", .to.data.frame = TRUE, .idx = 66666)` did not throw the expected error. [ FAIL 4 | WARN 7 | SKIP 0 | PASS 166 ] Error: Test failures Execution halted Flavor: r-devel-windows-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 Flavor: r-oldrel-macos-x86_64