* using log directory 'd:/RCompile/CRANincoming/R-devel/PubChemR.Rcheck' * using R Under development (unstable) (2024-07-11 r86890 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'PubChemR/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'PubChemR' version '2.0' * package encoding: UTF-8 * checking CRAN incoming feasibility ... Note_to_CRAN_maintainers Maintainer: 'Selcuk Korkmaz ' * 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 hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'PubChemR' can be installed ... OK * checking installed package size ... OK * 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 ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... 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 ... OK * checking Rd files ... 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 ... [13s] OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... [78s] ERROR Running 'testthat.R' [78s] 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\Rtmpy4anIi/aspirin.json' The file has been saved to 'D:\temp\Rtmpy4anIi/aspirin.json' The file has been saved to 'D:\temp\Rtmpy4anIi/aspirin.json' The file has been saved to 'D:\temp\Rtmpy4anIi/aspirin.json' The file has been saved to 'D:\temp\Rtmpy4anIi/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_2024-07-12_08_12_12.572221.sdf' Saved into folder --> D:\temp\Rtmpy4anIi 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 --> D:\temp\Rtmpy4anIi 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 --> D:\temp\Rtmpy4anIi Completed options PubChem Substance Details (comment) Same as: D00109 Is a reactant of enzyme EC: 3.1.1.55 PubChem Substance Details (comment) Same as: D00109 Is a reactant of enzyme EC: 3.1.1.55 [ FAIL 1 | WARN 0 | SKIP 0 | PASS 217 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-00_globals.R:103:3'): calculateObjectSize() works properly ─── { ... } is not TRUE `actual`: FALSE `expected`: TRUE [ FAIL 1 | WARN 0 | SKIP 0 | PASS 217 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [183s] OK * checking PDF version of manual ... [14s] OK * checking HTML version of manual ... OK * DONE Status: 1 ERROR