CRAN Package Check Results for Maintainer ‘Selcuk Korkmaz <selcukorkmaz at gmail.com>’

Last updated on 2025-12-04 09:50:33 CET.

Package	ERROR	OK
fastml		13
genSEIR		13
MVN		13
PubChemR	2	11
rPDBapi		13

Package fastml

Current CRAN status: OK: 13

Package genSEIR

Current CRAN status: OK: 13

Package MVN

Current CRAN status: OK: 13

Package PubChemR

Current CRAN status: ERROR: 2, OK: 11

Version: 2.1.7
Check: tests
Result: ERROR Running ‘testthat.R’ [9s/167s] 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/RtmpCor8cx/working_dir/Rtmptrgld3/aspirin.json' The file has been saved to '/tmp/RtmpCor8cx/working_dir/Rtmptrgld3/aspirin.json' The file has been saved to '/tmp/RtmpCor8cx/working_dir/Rtmptrgld3/aspirin.json' The file has been saved to '/tmp/RtmpCor8cx/working_dir/Rtmptrgld3/aspirin.json' The file has been saved to '/tmp/RtmpCor8cx/working_dir/Rtmptrgld3/aspirin.sdf' Request failed [400]. Retrying in 3.4 seconds... Request failed [400]. Retrying in 5.3 seconds... Request failed [504]. Retrying in 2.5 seconds... Saving _problems/test-get_sids-20.R Saving _problems/test-get_sids-53.R 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 Saving _problems/test-get_synonyms-6.R [ FAIL 3 | WARN 0 | SKIP 0 | PASS 158 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-get_sids.R:20:5'): pulling sids via 'name' is succesfull ───── Expected `allSuccess(object)` to be TRUE. Differences: `actual`: FALSE `expected`: TRUE ── Failure ('test-get_sids.R:53:3'): pulling sids for multiple identifiers with undefined input. ── Expected `sids$result[[1]]$success` to be TRUE. Differences: `actual`: FALSE `expected`: TRUE ── Failure ('test-get_synonyms.R:6:1'): pulling via 'name' is succesfull ─────── Expected `allSuccess(object)` to be TRUE. Differences: `actual`: FALSE `expected`: TRUE [ FAIL 3 | WARN 0 | SKIP 0 | PASS 158 ] Error: ! Test failures. Execution halted Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 2.1.7
Check: tests
Result: ERROR Running 'testthat.R' [59s] 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_12_02_01_50_00_12944\RtmpqWF3hS/aspirin.json' The file has been saved to 'D:\temp\2025_12_02_01_50_00_12944\RtmpqWF3hS/aspirin.json' The file has been saved to 'D:\temp\2025_12_02_01_50_00_12944\RtmpqWF3hS/aspirin.json' The file has been saved to 'D:\temp\2025_12_02_01_50_00_12944\RtmpqWF3hS/aspirin.json' The file has been saved to 'D:\temp\2025_12_02_01_50_00_12944\RtmpqWF3hS/aspirin.sdf' Saving _problems/test-get_pug_rest-30.R Saving _problems/test-get_pug_rest-32.R Request failed [400]. Retrying in 1 seconds... Request failed [400]. Retrying in 4.7 seconds... 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 2 | SKIP 0 | PASS 159 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-get_pug_rest.R:28:3'): tests for SDF output successful ─────── Expected `{ ... }` to be TRUE. Differences: `actual`: FALSE `expected`: TRUE ── Failure ('test-get_pug_rest.R:32:3'): tests for SDF output successful ─────── Expected `all(is.list(pubChemData(tmp)), length(pubChemData(tmp)) == 0)` to be TRUE. Differences: `actual`: FALSE `expected`: TRUE [ FAIL 2 | WARN 2 | SKIP 0 | PASS 159 ] Error: ! Test failures. Execution halted Flavor: r-devel-windows-x86_64

Package rPDBapi

Current CRAN status: OK: 13