• using R version 4.5.1 Patched (2025-09-22 r88868)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-14 (Debian 14.3.0-8) 14.3.0     GNU Fortran (Debian 14.3.0-8) 14.3.0
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8
• checking for file ‘PubChemR/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘PubChemR’ version ‘2.1.5’
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking whether package ‘PubChemR’ can be installed ... OK See the install log for details.
• checking package directory ... OK
• checking for future file timestamps ... OK
• checking ‘build’ directory ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
• checking for left-over files ... OK
• checking index information ... OK
• checking package subdirectories ... OK
• checking code files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... [2s/2s] OK
• checking whether the package can be loaded with stated dependencies ... [1s/2s] OK
• checking whether the package can be unloaded cleanly ... [1s/1s] OK
• checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
• checking whether the namespace can be unloaded cleanly ... [2s/2s] OK
• checking loading without being on the library search path ... [2s/2s] OK
• checking use of S3 registration ... OK
• checking dependencies in R code ... OK
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... [13s/16s] OK
• checking Rd files ... [1s/1s] OK
• checking Rd metadata ... OK
• checking Rd line widths ... OK
• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
• checking Rd contents ... OK
• checking for unstated dependencies in examples ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [5s/72s] OK Examples with CPU (user + system) or elapsed time > 5s                 user system elapsed AIDs-SIDs-CIDs 0.485 0.118 30.194 get_assays 0.051 0.001 28.644
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [7s/94s] 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
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [104s/395s] OK
• checking PDF version of manual ... [7s/11s] OK
• checking HTML version of manual ... [2s/2s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR