Check results for 'PubChemR'

using R Under development (unstable) (2024-12-15 r87442)
using platform: x86_64-pc-linux-gnu
R was compiled by Debian clang version 19.1.4 (1) Debian flang-new version 19.1.4 (1)
running under: Debian GNU/Linux trixie/sid
using session charset: UTF-8
checking for file ‘PubChemR/DESCRIPTION’ ... OK
checking extension type ... Package
this is package ‘PubChemR’ version ‘2.1.1’
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/1s] OK
checking whether the package can be unloaded cleanly ... [1s/2s] 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/3s] 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 ... [14s/17s] 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/16s] OK
checking for unstated dependencies in ‘tests’ ... OK
checking tests ... [7s/54s] ERROR Running ‘testthat.R’ [7s/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 '/home/hornik/tmp/scratch/Rtmp94JpzK/aspirin.json' The file has been saved to '/home/hornik/tmp/scratch/Rtmp94JpzK/aspirin.json' The file has been saved to '/home/hornik/tmp/scratch/Rtmp94JpzK/aspirin.json' The file has been saved to '/home/hornik/tmp/scratch/Rtmp94JpzK/aspirin.json' The file has been saved to '/home/hornik/tmp/scratch/Rtmp94JpzK/aspirin.sdf' Request failed [400]. Retrying in 1 seconds... Request failed [400]. Retrying in 5.1 seconds... SDF file saved successfully: File Name: 'aspirin_20241216_182515.sdf' Saved at: /home/hornik/tmp/scratch/Rtmp94JpzK SDF file saved successfully: File Name: 'file.sdf' Saved at: /home/hornik/tmp/scratch/Rtmp94JpzK 'path' is not specified. Saving files into a temporary folder. SDF file saved successfully: File Name: 'file.sdf' Saved at: /home/hornik/tmp/scratch/Rtmp94JpzK 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 0 | SKIP 1 | PASS 201 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • empty test (1): 'test-00_globals.R:21:1' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-get_substances.R:45:3'): NULL returns for unknown/empty slots. ── retrieve(tmp, .slot = "comment", .to.data.frame = TRUE, .idx = 132) is not NULL `actual` is an S3 object of class <tbl_df/tbl/data.frame>, a list `expected` is NULL [ FAIL 1 | WARN 0 | SKIP 1 | PASS 201 ] Error: Test failures Execution halted
checking for unstated dependencies in vignettes ... OK
checking package vignettes ... OK
checking re-building of vignette outputs ... [106s/211s] OK
checking PDF version of manual ... [7s/9s] OK
checking HTML version of manual ... [2s/3s] OK
checking for non-standard things in the check directory ... OK
DONE

Status: 1 ERROR