CRAN Package Check Results for Package PubChemR

Last updated on 2024-09-12 15:49:36 CEST.

Flavor	Version	T_install	T_check	T_total	Status
r-devel-linux-x86_64-debian-clang	2.0.1	7.03	177.73	184.76	ERROR
r-devel-linux-x86_64-debian-gcc	2.0.1	5.36	121.28	126.64	OK
r-devel-linux-x86_64-fedora-clang	2.0.1			302.73	OK
r-devel-linux-x86_64-fedora-gcc	2.0.1			302.01	OK
r-devel-windows-x86_64	2.0.1	10.00	286.00	296.00	OK
r-patched-linux-x86_64	2.0.1	7.54	168.55	176.09	ERROR
r-release-linux-x86_64	2.0.1	7.55	168.60	176.15	OK
r-release-macos-arm64	2.0.1			261.00	OK
r-release-macos-x86_64	2.0.1			471.00	OK
r-release-windows-x86_64	2.0.1	9.00	353.00	362.00	OK
r-oldrel-macos-arm64	2.0.1			414.00	OK
r-oldrel-macos-x86_64	2.0.1			591.00	OK
r-oldrel-windows-x86_64	2.0.1	12.00	268.00	280.00	OK

Check Details

Version: 2.0.1
Check: tests
Result: ERROR Running ‘testthat.R’ [8s/56s] 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/RtmpCCCYTb/aspirin.json' The file has been saved to '/home/hornik/tmp/scratch/RtmpCCCYTb/aspirin.json' The file has been saved to '/home/hornik/tmp/scratch/RtmpCCCYTb/aspirin.json' The file has been saved to '/home/hornik/tmp/scratch/RtmpCCCYTb/aspirin.json' Error in file(con, "r") : cannot open the connection trying URL 'https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/2244/SDF' downloaded 3641 bytes trying URL 'https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/2244/SDF' downloaded 3641 bytes trying URL 'https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/aspirin/SDF' downloaded 3641 bytes SDF file to save --> 'aspirin_2024-09-09_18_08_03.974231.sdf' Saved into folder --> /home/hornik/tmp/scratch/RtmpCCCYTb Completed options trying URL 'https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/2244/SDF' downloaded 3641 bytes SDF file to save --> 'file.sdf' Saved into folder --> /home/hornik/tmp/scratch/RtmpCCCYTb Completed options 'path' is not specified. Saving files into a temporary folder. trying URL 'https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/aspirin/SDF' downloaded 3641 bytes SDF file to save --> 'file.sdf' Saved into folder --> /home/hornik/tmp/scratch/RtmpCCCYTb Completed options 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 1 | SKIP 0 | PASS 204 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-download.R:119:3'): create 'path' if it does not exist. ────── all(file.exists(json_file), file.exists(sdf_file)) is not TRUE `actual`: FALSE `expected`: TRUE [ FAIL 1 | WARN 1 | SKIP 0 | PASS 204 ] Error: Test failures Execution halted Flavor: r-devel-linux-x86_64-debian-clang

Version: 2.0.1
Check: tests
Result: ERROR Running ‘testthat.R’ [8s/47s] 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/Rtmpz11pHn/aspirin.json' The file has been saved to '/home/hornik/tmp/scratch/Rtmpz11pHn/aspirin.json' The file has been saved to '/home/hornik/tmp/scratch/Rtmpz11pHn/aspirin.json' The file has been saved to '/home/hornik/tmp/scratch/Rtmpz11pHn/aspirin.json' The file has been saved to '/home/hornik/tmp/scratch/Rtmpz11pHn/aspirin.sdf' trying URL 'https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/2244/SDF' downloaded 3641 bytes trying URL 'https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/2244/SDF' downloaded 3641 bytes trying URL 'https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/aspirin/SDF' downloaded 3641 bytes SDF file to save --> 'aspirin_2024-09-10_18_20_49.876158.sdf' Saved into folder --> /home/hornik/tmp/scratch/Rtmpz11pHn Completed options trying URL 'https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/2244/SDF' downloaded 3641 bytes SDF file to save --> 'file.sdf' Saved into folder --> /home/hornik/tmp/scratch/Rtmpz11pHn Completed options 'path' is not specified. Saving files into a temporary folder. trying URL 'https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/aspirin/SDF' downloaded 3641 bytes SDF file to save --> 'file.sdf' Saved into folder --> /home/hornik/tmp/scratch/Rtmpz11pHn Completed options 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 203 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-get_aids.R:20:5'): pulling aids via 'cid' is succesfull ────── allSuccess(object) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-get_aids.R:24:5'): AIDs succesfully returns 'data.frame' and 'list' ── { ... } is not TRUE `actual`: FALSE `expected`: TRUE Backtrace: ▆ 1. └─PubChemR (local) toDataFrame(object) at test-get_aids.R:24:5 2. └─testthat::expect_true(...) at test-get_aids.R:5:3 [ FAIL 2 | WARN 0 | SKIP 0 | PASS 203 ] Error: Test failures Execution halted Flavor: r-patched-linux-x86_64