CRAN Package Check Results for Package PubChemR

Last updated on 2025-01-18 04:48:33 CET.

Flavor	Version	T_install	T_check	T_total	Status
r-devel-linux-x86_64-debian-clang	2.1.3	8.24	176.94	185.18	ERROR
r-devel-linux-x86_64-debian-gcc	2.1.3	5.37	118.26	123.63	OK
r-devel-linux-x86_64-fedora-clang	2.1.3			302.44	OK
r-devel-linux-x86_64-fedora-gcc	2.1.3			325.38	OK
r-devel-windows-x86_64	2.1.3	12.00	340.00	352.00	OK
r-patched-linux-x86_64	2.1.3	8.49	165.78	174.27	OK
r-release-linux-x86_64	2.1.3	6.43	166.19	172.62	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	11.00	300.00	311.00	OK
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	11.00	382.00	393.00	ERROR

Check Details

Version: 2.1.3
Check: examples
Result: ERROR Running examples in ‘PubChemR-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: download > ### Title: Download Content from PubChem and Save to a File > ### Aliases: download > > ### ** Examples > > # Download JSON file for the compound "aspirin" into "Aspirin.JSON" > # A folder named "Compound" will be created under current directory" > download( + filename = "Aspirin", + outformat = "json", + path = "./Compound", + identifier = "aspirin", + namespace = "name", + domain = "compound", + overwrite = TRUE + ) Error in curl::curl_fetch_memory(url, handle = handle) : Timeout was reached [pubchem.ncbi.nlm.nih.gov]: Resolving timed out after 10001 milliseconds Calls: download ... request_fetch.write_memory -> <Anonymous> -> raise_libcurl_error Execution halted Examples with CPU (user + system) or elapsed time > 5s user system elapsed AIDs-SIDs-CIDs 0.174 0.002 145.351 Flavor: r-devel-linux-x86_64-debian-clang

Version: 2.1.3
Check: tests
Result: ERROR Running ‘testthat.R’ [8s/188s] 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") + } Error in curl::curl_fetch_memory(url, handle = handle) : Timeout was reached [pubchem.ncbi.nlm.nih.gov]: Resolving timed out after 10000 milliseconds The file has been saved to '/home/hornik/tmp/scratch/Rtmp2txSXR/aspirin.json' The file has been saved to '/home/hornik/tmp/scratch/Rtmp2txSXR/aspirin.json' The file has been saved to '/home/hornik/tmp/scratch/Rtmp2txSXR/aspirin.json' The file has been saved to '/home/hornik/tmp/scratch/Rtmp2txSXR/aspirin.sdf' Request failed [400]. Retrying in 1.2 seconds... Request failed [400]. Retrying in 4.6 seconds... SDF file saved successfully: File Name: 'aspirin_20250116_183631.sdf' Saved at: /home/hornik/tmp/scratch/Rtmp2txSXR SDF file saved successfully: File Name: 'file.sdf' Saved at: /home/hornik/tmp/scratch/Rtmp2txSXR 'path' is not specified. Saving files into a temporary folder. SDF file saved successfully: File Name: 'file.sdf' Saved at: /home/hornik/tmp/scratch/Rtmp2txSXR 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 3 | WARN 1 | SKIP 0 | PASS 198 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-00_globals.R:66:3'): succesfully returned primary class of given object ── primaryClass(instance(tmp)) (`actual`) not equal to "PubChemInstance" (`expected`). `actual`: "NULL" `expected`: "PubChemInstance" ── Error ('test-00_globals.R:83:3'): slot details successfully printed ───────── <subscriptOutOfBoundsError/error/condition> Error in `x[[1]]`: subscript out of bounds Backtrace: ▆ 1. ├─testthat::expect_output(printSlotDetails(find_last_layer(pview$result))) at test-00_globals.R:83:3 2. │ └─testthat:::quasi_capture(...) 3. │ ├─testthat (local) .capture(...) 4. │ │ └─testthat::capture_output_lines(code, print, width = width) 5. │ │ └─testthat:::eval_with_output(code, print = print, width = width) 6. │ │ ├─withr::with_output_sink(path, withVisible(code)) 7. │ │ │ └─base::force(code) 8. │ │ └─base::withVisible(code) 9. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 10. ├─PubChemR:::printSlotDetails(find_last_layer(pview$result)) 11. └─PubChemR:::find_last_layer(pview$result) ── Error ('test-00_globals.R:90:3'): section details successfully printed ────── Error in `UseMethod("section")`: no applicable method for 'section' applied to an object of class "NULL" Backtrace: ▆ 1. ├─PubChemR::section(pview, "S1") at test-00_globals.R:90:3 2. └─PubChemR:::section.PugViewInstance(pview, "S1") 3. ├─base::do.call("section", call_args) 4. └─PubChemR::section(object = NULL, .id = "S1", .verbose = FALSE) [ FAIL 3 | WARN 1 | SKIP 0 | PASS 198 ] Error: Test failures Execution halted Flavor: r-devel-linux-x86_64-debian-clang

Version: 2.1.3
Check: for non-standard things in the check directory
Result: NOTE Found the following files/directories: ‘Compound’ Flavor: r-devel-linux-x86_64-debian-clang

Version: 2.1.3
Check: tests
Result: ERROR Running 'testthat.R' [72s] 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_01_15_01_50_00_14816\Rtmp88M0iT/aspirin.json' The file has been saved to 'D:\temp\2025_01_15_01_50_00_14816\Rtmp88M0iT/aspirin.json' The file has been saved to 'D:\temp\2025_01_15_01_50_00_14816\Rtmp88M0iT/aspirin.json' The file has been saved to 'D:\temp\2025_01_15_01_50_00_14816\Rtmp88M0iT/aspirin.json' The file has been saved to 'D:\temp\2025_01_15_01_50_00_14816\Rtmp88M0iT/aspirin.sdf' Request failed [400]. Retrying in 1 seconds... Request failed [400]. Retrying in 3 seconds... SDF file saved successfully: File Name: 'aspirin_20250115_084011.sdf' Saved at: D:\temp\2025_01_15_01_50_00_14816\Rtmp88M0iT SDF file saved successfully: File Name: 'file.sdf' Saved at: D:\temp\2025_01_15_01_50_00_14816\Rtmp88M0iT 'path' is not specified. Saving files into a temporary folder. SDF file saved successfully: File Name: 'file.sdf' Saved at: D:\temp\2025_01_15_01_50_00_14816\Rtmp88M0iT 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_cids.R:24:5'): CIDs succesfully returns 'data.frame' and 'list' ── { ... } is not TRUE `actual`: FALSE `expected`: TRUE Backtrace: ▆ 1. └─PubChemR (local) toDataFrame(object) at test-get_cids.R:24:5 2. └─testthat::expect_true(...) at test-get_cids.R:12:3 [ FAIL 1 | WARN 0 | SKIP 0 | PASS 203 ] Error: Test failures Execution halted Flavor: r-oldrel-windows-x86_64