CRAN Package Check Results for Package PubChemR

Last updated on 2025-09-26 02:49:46 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2.1.5 7.60 181.34 188.94 OK
r-devel-linux-x86_64-debian-gcc 2.1.5 5.51 115.86 121.37 ERROR
r-devel-linux-x86_64-fedora-clang 2.1.5 294.29 OK
r-devel-linux-x86_64-fedora-gcc 2.1.5 302.82 OK
r-devel-windows-x86_64 2.1.5 10.00 324.00 334.00 OK
r-patched-linux-x86_64 2.1.5 6.56 171.09 177.65 ERROR
r-release-linux-x86_64 2.1.5 7.26 173.24 180.50 OK
r-release-macos-arm64 2.1.5 247.00 OK
r-release-macos-x86_64 2.1.5 385.00 OK
r-release-windows-x86_64 2.1.5 10.00 388.00 398.00 OK
r-oldrel-macos-arm64 2.1.5 260.00 NOTE
r-oldrel-macos-x86_64 2.1.5 461.00 NOTE
r-oldrel-windows-x86_64 2.1.5 15.00 619.00 634.00 ERROR

Check Details

Version: 2.1.5
Check: tests
Result: ERROR Running ‘testthat.R’ [4s/81s] 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/RtmpLSFlYY/aspirin.json' The file has been saved to '/tmp/RtmpLSFlYY/aspirin.json' The file has been saved to '/tmp/RtmpLSFlYY/aspirin.json' The file has been saved to '/tmp/RtmpLSFlYY/aspirin.json' The file has been saved to '/tmp/RtmpLSFlYY/aspirin.sdf' Request failed [400]. Retrying in 1 seconds... Request failed [400]. Retrying in 7.7 seconds... SDF file saved successfully: File Name: 'aspirin_20250925_135549.sdf' Saved at: /tmp/RtmpLSFlYY SDF file saved successfully: File Name: 'file.sdf' Saved at: /tmp/RtmpLSFlYY 'path' is not specified. Saving files into a temporary folder. SDF file saved successfully: File Name: 'file.sdf' Saved at: /tmp/RtmpLSFlYY 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_sids.R:20:5'): pulling sids via 'cid' 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-linux-x86_64-debian-gcc

Version: 2.1.5
Check: tests
Result: ERROR Running ‘testthat.R’ [6s/94s] 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 '/home/hornik/tmp/scratch/RtmpRb0O60/aspirin.json' The file has been saved to '/home/hornik/tmp/scratch/RtmpRb0O60/aspirin.json' The file has been saved to '/home/hornik/tmp/scratch/RtmpRb0O60/aspirin.json' The file has been saved to '/home/hornik/tmp/scratch/RtmpRb0O60/aspirin.json' The file has been saved to '/home/hornik/tmp/scratch/RtmpRb0O60/aspirin.sdf' Request failed [400]. Retrying in 2.4 seconds... Request failed [400]. Retrying in 1 seconds... SDF file saved successfully: File Name: 'aspirin_20250924_072604.sdf' Saved at: /home/hornik/tmp/scratch/RtmpRb0O60 SDF file saved successfully: File Name: 'file.sdf' Saved at: /home/hornik/tmp/scratch/RtmpRb0O60 'path' is not specified. Saving files into a temporary folder. SDF file saved successfully: File Name: 'file.sdf' Saved at: /home/hornik/tmp/scratch/RtmpRb0O60 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 4 | WARN 9 | SKIP 0 | PASS 166 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-get_assays.R:5:1'): pulling via 'aid' is succesfull ────────── allSuccess(object) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-get_assays.R:42:3'): retrieve() returns selected slots as expected for an assay ── { ... } is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-get_assays.R:61:3'): checking the effect of '.verbose' argument in retrieve() function ── `retrieve(assay, .slot = "comment", .verbose = TRUE)` produced no output ── 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 4 | WARN 9 | SKIP 0 | PASS 166 ] Error: Test failures Execution halted Flavor: r-patched-linux-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 Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64

Version: 2.1.5
Check: tests
Result: ERROR Running 'testthat.R' [163s] 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_24_01_50_00_30071\RtmpSESehE/aspirin.json' The file has been saved to 'D:\temp\2025_09_24_01_50_00_30071\RtmpSESehE/aspirin.json' The file has been saved to 'D:\temp\2025_09_24_01_50_00_30071\RtmpSESehE/aspirin.json' The file has been saved to 'D:\temp\2025_09_24_01_50_00_30071\RtmpSESehE/aspirin.json' The file has been saved to 'D:\temp\2025_09_24_01_50_00_30071\RtmpSESehE/aspirin.sdf' Request failed [400]. Retrying in 1 seconds... Request failed [400]. Retrying in 6.4 seconds... Request failed [504]. Retrying in 1 seconds... Request failed [504]. Retrying in 1.2 seconds... SDF file saved successfully: File Name: 'aspirin_20250924_095627.sdf' Saved at: D:\temp\2025_09_24_01_50_00_30071\RtmpSESehE SDF file saved successfully: File Name: 'file.sdf' Saved at: D:\temp\2025_09_24_01_50_00_30071\RtmpSESehE 'path' is not specified. Saving files into a temporary folder. SDF file saved successfully: File Name: 'file.sdf' Saved at: D:\temp\2025_09_24_01_50_00_30071\RtmpSESehE 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 4 | WARN 9 | SKIP 0 | PASS 166 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-get_assays.R:5:1'): pulling via 'aid' is succesfull ────────── allSuccess(object) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-get_assays.R:42:3'): retrieve() returns selected slots as expected for an assay ── { ... } is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-get_assays.R:61:3'): checking the effect of '.verbose' argument in retrieve() function ── `retrieve(assay, .slot = "comment", .verbose = TRUE)` produced no output ── Failure ('test-get_sids.R:20:5'): pulling sids via 'name' is succesfull ───── allSuccess(object) is not TRUE `actual`: FALSE `expected`: TRUE [ FAIL 4 | WARN 9 | SKIP 0 | PASS 166 ] Error: Test failures Execution halted Flavor: r-oldrel-windows-x86_64