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

Last updated on 2025-04-24 21:51:34 CEST.

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: 2.1.4
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: --- re-building 'Enhancing_Chemical_Data_Access_with_PubChemR.Rmd' using rmarkdown --- finished re-building 'Enhancing_Chemical_Data_Access_with_PubChemR.Rmd' --- re-building 'Exploring_Chemical_Data_with_PubChemR.Rmd' using rmarkdown --- finished re-building 'Exploring_Chemical_Data_with_PubChemR.Rmd' --- re-building 'Working_with_PubChemR_to_Access_Chemical_Data.Rmd' using rmarkdown Quitting from Working_with_PubChemR_to_Access_Chemical_Data.Rmd:1038-1048 [download_jsson] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `curl::curl_fetch_memory()`: ! Could not connect to server [pubchem.ncbi.nlm.nih.gov]: Failed to connect to pubchem.ncbi.nlm.nih.gov port 443 after 9929 ms: Could not connect to server --- Backtrace: ▆ 1. ├─PubChemR::download(...) 2. │ └─PubChemR:::get_pubchem(...) 3. │ └─httr::GET(...) 4. │ └─httr:::request_perform(req, hu$handle$handle) 5. │ ├─httr:::request_fetch(req$output, req$url, handle) 6. │ └─httr:::request_fetch.write_memory(req$output, req$url, handle) 7. │ └─curl::curl_fetch_memory(url, handle = handle) 8. └─curl:::raise_libcurl_error(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'Working_with_PubChemR_to_Access_Chemical_Data.Rmd' failed with diagnostics: Could not connect to server [pubchem.ncbi.nlm.nih.gov]: Failed to connect to pubchem.ncbi.nlm.nih.gov port 443 after 9929 ms: Could not connect to server --- failed re-building 'Working_with_PubChemR_to_Access_Chemical_Data.Rmd' SUMMARY: processing the following file failed: 'Working_with_PubChemR_to_Access_Chemical_Data.Rmd' Error: Vignette re-building failed. Execution halted Flavor: r-devel-windows-x86_64

Version: 2.1.4
Check: tests
Result: ERROR Running 'testthat.R' [53s] 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_04_23_01_50_01_29948\RtmpyeKL7E/aspirin.json' The file has been saved to 'D:\temp\2025_04_23_01_50_01_29948\RtmpyeKL7E/aspirin.json' The file has been saved to 'D:\temp\2025_04_23_01_50_01_29948\RtmpyeKL7E/aspirin.json' The file has been saved to 'D:\temp\2025_04_23_01_50_01_29948\RtmpyeKL7E/aspirin.json' The file has been saved to 'D:\temp\2025_04_23_01_50_01_29948\RtmpyeKL7E/aspirin.sdf' Error in value[[3L]](cond) : Failed to retrieve sources for the specified domain: c(Code = "PUGREST.ServerBusy", Message = "Too many requests or server too busy") Request failed [400]. Retrying in 3.1 seconds... Request failed [400]. Retrying in 2.4 seconds... SDF file saved successfully: File Name: 'aspirin_20250423_091258.sdf' Saved at: D:\temp\2025_04_23_01_50_01_29948\RtmpyeKL7E SDF file saved successfully: File Name: 'file.sdf' Saved at: D:\temp\2025_04_23_01_50_01_29948\RtmpyeKL7E 'path' is not specified. Saving files into a temporary folder. SDF file saved successfully: File Name: 'file.sdf' Saved at: D:\temp\2025_04_23_01_50_01_29948\RtmpyeKL7E 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:9:3'): get all sources for 'substance' ───── inherits(tmp, "try-error") is not FALSE `actual`: TRUE `expected`: FALSE ── Failure ('test-get_all_sources.R:10:3'): get all sources for 'substance' ──── all(...) is not TRUE `actual`: FALSE `expected`: TRUE [ FAIL 2 | WARN 0 | SKIP 0 | PASS 168 ] Error: Test failures Execution halted Flavor: r-release-windows-x86_64

Package rPDBapi

Current CRAN status: OK: 13