• using R Under development (unstable) (2025-02-20 r87772)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-14 (Debian 14.2.0-16) 14.2.0     GNU Fortran (Debian 14.2.0-16) 14.2.0
• 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 ‘2.1.3’
• 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 ... [1s/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 ... [1s/2s] OK
• checking loading without being on the library search path ... [1s/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 ... [9s/12s] OK
• checking Rd files ... [0s/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 ... [1s/72s] ERROR Running examples in ‘PubChemR-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: download > ### Title: Download Content from PubChem and Save to a File > ### Aliases: download > > ### ** Examples > > # Download JSON file for the compound "aspirin" into "Aspirin.JSON" > # A folder named "Compound" will be created under current directory" > download( + filename = "Aspirin", + outformat = "json", + path = "./Compound", + identifier = "aspirin", + namespace = "name", + domain = "compound", + overwrite = TRUE + ) Error in curl::curl_fetch_memory(url, handle = handle) :   Timeout was reached [pubchem.ncbi.nlm.nih.gov]: Resolving timed out after 10000 milliseconds Calls: download ... request_fetch.write_memory -> <Anonymous> -> raise_libcurl_error Execution halted Examples with CPU (user + system) or elapsed time > 5s                 user system elapsed AIDs-SIDs-CIDs 0.087 0.021 60.156
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [5s/358s] ERROR   Running ‘testthat.R’ [5s/358s] 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")   + }   Error in curl::curl_fetch_memory(url, handle = handle) :     Timeout was reached [pubchem.ncbi.nlm.nih.gov]: Resolving timed out after 10000 milliseconds   Error in curl::curl_fetch_memory(url, handle = handle) :     Timeout was reached [pubchem.ncbi.nlm.nih.gov]: Resolving timed out after 10000 milliseconds   Error in curl::curl_fetch_memory(url, handle = handle) :     Timeout was reached [pubchem.ncbi.nlm.nih.gov]: Resolving timed out after 10000 milliseconds   Error in curl::curl_fetch_memory(url, handle = handle) :     Timeout was reached [pubchem.ncbi.nlm.nih.gov]: Connection timed out after 10000 milliseconds   The file has been saved to '/tmp/RtmpBnDmiI/aspirin.sdf'      Request failed [400]. Retrying in 3.3 seconds...   Request failed [400]. Retrying in 1 seconds...   SDF file saved successfully:     File Name: 'aspirin_20250221_134939.sdf'     Saved at: /tmp/RtmpBnDmiI   SDF file saved successfully:     File Name: 'file.sdf'     Saved at: /tmp/RtmpBnDmiI   'path' is not specified. Saving files into a temporary folder.   SDF file saved successfully:     File Name: 'file.sdf'     Saved at: /tmp/RtmpBnDmiI   Failed to retrieve synonyms for identifier 'aspirin': <text>:1:9: unexpected symbol   1: Timeout was               ^   Failed to retrieve synonyms for identifier 'ibuprofen': <text>:1:9: unexpected symbol   1: Timeout was               ^   Failed to retrieve synonyms for identifier 'aspirin': <text>:1:9: unexpected symbol   1: Timeout was               ^   Failed to retrieve synonyms for identifier '2244': <text>:1:9: unexpected symbol   1: Timeout was               ^   Failed to retrieve synonyms for identifier 'dncr': <text>:1:9: unexpected symbol   1: Timeout was               ^   [ FAIL 22 | WARN 11 | SKIP 0 | PASS 179 ]      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Failure ('test-00_globals.R:66:3'): succesfully returned primary class of given object ──   primaryClass(instance(tmp)) (`actual`) not equal to "PubChemInstance" (`expected`).      `actual`: "NULL"   `expected`: "PubChemInstance"   ── Error ('test-00_globals.R:83:3'): slot details successfully printed ─────────   <subscriptOutOfBoundsError/error/condition>   Error in `x[[1]]`: subscript out of bounds   Backtrace:        ▆     1. ├─testthat::expect_output(printSlotDetails(find_last_layer(pview$result))) at test-00_globals.R:83:3     2. │ └─testthat:::quasi_capture(...)     3. │ ├─testthat (local) .capture(...)     4. │ │ └─testthat::capture_output_lines(code, print, width = width)     5. │ │ └─testthat:::eval_with_output(code, print = print, width = width)     6. │ │ ├─withr::with_output_sink(path, withVisible(code))     7. │ │ │ └─base::force(code)     8. │ │ └─base::withVisible(code)     9. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))    10. ├─PubChemR:::printSlotDetails(find_last_layer(pview$result))    11. └─PubChemR:::find_last_layer(pview$result)   ── Error ('test-00_globals.R:90:3'): section details successfully printed ──────   Error in `UseMethod("section")`: no applicable method for 'section' applied to an object of class "NULL"   Backtrace:       ▆    1. ├─PubChemR::section(pview, "S1") at test-00_globals.R:90:3    2. └─PubChemR:::section.PugViewInstance(pview, "S1")    3. ├─base::do.call("section", call_args)    4. └─PubChemR::section(object = NULL, .id = "S1", .verbose = FALSE)   ── Failure ('test-download.R:51:5'): overwrite file if it already exists. ──────   identical(ctime, mtime) is not FALSE      `actual`: TRUE   `expected`: FALSE   ── Failure ('test-download.R:119:3'): create 'path' if it does not exist. ──────   all(file.exists(json_file), file.exists(sdf_file)) is not TRUE      `actual`: FALSE   `expected`: TRUE   ── Failure ('test-get_sids.R:24:5'): SIDs succesfully returns 'data.frame' and 'list' ──   {       ...   } is not TRUE      `actual`: FALSE   `expected`: TRUE   Backtrace:       ▆    1. └─PubChemR (local) toDataFrame(object) at test-get_sids.R:24:5    2. └─testthat::expect_true(...) at test-get_sids.R:5:3   ── Failure ('test-get_sids.R:24:5'): SIDs succesfully returns 'data.frame' and 'list' ──   {       ...   } is not TRUE      `actual`: FALSE   `expected`: TRUE   Backtrace:       ▆    1. └─PubChemR (local) toDataFrame(object) at test-get_sids.R:24:5    2. └─testthat::expect_true(...) at test-get_sids.R:5:3   ── Failure ('test-get_sids.R:24:5'): SIDs succesfully returns 'data.frame' and 'list' ──   {       ...   } is not TRUE      `actual`: FALSE   `expected`: TRUE   Backtrace:       ▆    1. └─PubChemR (local) toDataFrame(object) at test-get_sids.R:24:5    2. └─testthat::expect_true(...) at test-get_sids.R:5:3   ── Failure ('test-get_sids.R:53:3'): pulling sids for multiple identifiers with undefined input. ──   sids$result[[1]]$success is not TRUE      `actual` is NULL   `expected` is a logical vector (TRUE)   ── Failure ('test-get_sids.R:54:3'): pulling sids for multiple identifiers with undefined input. ──   sids$result[[2]]$success is not FALSE      `actual` is NULL   `expected` is a logical vector (FALSE)   ── Failure ('test-get_sids.R:63:3'): undefined/incorrect identifier returns error ──   sids$result[[1]]$success is not FALSE      `actual` is NULL   `expected` is a logical vector (FALSE)   ── Failure ('test-get_sids.R:64:3'): undefined/incorrect identifier returns error ──   !is.null(sids$result[[1]]$error) is not TRUE      `actual`: FALSE   `expected`: TRUE   ── Failure ('test-get_substances.R:10:3'): instance() is succesfull. ───────────   `print\(instance\(subs, "aspirin"\)\)` does not match "Substance Data from PubChem Database".   Actual value: "NULL"   Backtrace:       ▆    1. └─testthat::expect_output(print(instance(subs, "aspirin")), "Substance Data from PubChem Database") at test-get_substances.R:10:3    2. └─testthat::expect_match(...)    3. └─testthat:::expect_match_(...)   ── Failure ('test-get_substances.R:27:3'): incorrect/undefined substance identifier returns error ──   {       ...   } is not FALSE      `actual`: TRUE   `expected`: FALSE   ── Failure ('test-get_substances.R:30:3'): incorrect/undefined substance identifier returns error ──   all(!is.null(tmp$result[[1]]$error), is.list(tmp$result[[1]]$error)) is not TRUE      `actual`: FALSE   `expected`: TRUE   ── Failure ('test-get_substances.R:36:3'): '.verbose' works as expected ────────   retrieve(...) returns invisibly, not visibly.   ── Failure ('test-get_substances.R:39:3'): '.verbose' works as expected ────────   retrieve(...) returns invisibly, not visibly.   ── Failure ('test-get_substances.R:45:3'): NULL returns for unknown/empty slots. ──   retrieve(...) is not NULL      `actual` is a character vector ('The object passed to \'retrieve\' is NULL. Please provide a valid object of the expected class.')   `expected` is NULL   ── Failure ('test-get_substances.R:50:3'): return error for unavailable substance idx. ──   `retrieve(tmp, .slot = "comment", .to.data.frame = TRUE, .idx = 66666)` did not throw the expected error.   ── Failure ('test-get_synonyms.R:10:3'): synonyms returns list or data.frame correctly ──   {       ...   } is not TRUE      `actual`: FALSE   `expected`: TRUE   ── Failure ('test-get_synonyms.R:59:3'): return error for incomplete/unknown identifiers ──   allSuccess(tmp) is not FALSE      `actual`: TRUE   `expected`: FALSE   ── Failure ('test-get_synonyms.R:60:3'): return error for incomplete/unknown identifiers ──   is.null(tmp$result[[1]]$error) is not FALSE      `actual`: TRUE   `expected`: FALSE      [ FAIL 22 | WARN 11 | SKIP 0 | PASS 179 ]   Error: Test failures   Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [63s/279s] ERROR Error(s) in re-building vignettes:   ... --- re-building ‘Enhancing_Chemical_Data_Access_with_PubChemR.Rmd’ using rmarkdown Quitting from lines 108-109 [unnamed-chunk-9] (Enhancing_Chemical_Data_Access_with_PubChemR.Rmd) Error: processing vignette 'Enhancing_Chemical_Data_Access_with_PubChemR.Rmd' failed with diagnostics: no applicable method for 'sectionList' applied to an object of class "NULL" --- failed 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 --- finished re-building ‘Working_with_PubChemR_to_Access_Chemical_Data.Rmd’ SUMMARY: processing the following file failed:   ‘Enhancing_Chemical_Data_Access_with_PubChemR.Rmd’ Error: Vignette re-building failed. Execution halted
• checking PDF version of manual ... [5s/7s] OK
• checking HTML version of manual ... [1s/1s] OK
• checking for non-standard things in the check directory ... NOTE Found the following files/directories:   ‘Compound’
• DONE

Status: 3 ERRORs, 1 NOTE