CRAN Package Check Results for Package PubChemR

Last updated on 2025-07-27 20:50:07 CEST.

Flavor	Version	T_install	T_check	T_total	Status
r-devel-linux-x86_64-debian-clang	2.1.4	7.51	178.85	186.36	OK
r-devel-linux-x86_64-debian-gcc	2.1.4	5.30	72.78	78.08	OK
r-devel-linux-x86_64-fedora-clang	2.1.4			290.03	OK
r-devel-linux-x86_64-fedora-gcc	2.1.4			174.60	OK
r-devel-windows-x86_64	2.1.4	11.00	314.00	325.00	OK
r-patched-linux-x86_64	2.1.4	8.46	170.19	178.65	OK
r-release-linux-x86_64	2.1.4	5.71	88.65	94.36	ERROR
r-release-macos-arm64	2.1.4			326.00	OK
r-release-macos-x86_64	2.1.4			283.00	OK
r-release-windows-x86_64	2.1.4	11.00	149.00	160.00	ERROR
r-oldrel-macos-arm64	2.1.4			221.00	OK
r-oldrel-macos-x86_64	2.1.4			312.00	OK
r-oldrel-windows-x86_64	2.1.4	14.00	369.00	383.00	OK

Check Details

Version: 2.1.4
Check: examples
Result: ERROR Running examples in ‘PubChemR-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: get_all_sources > ### Title: Retrieve All Sources from PubChem > ### Aliases: get_all_sources > > ### ** Examples > > get_all_sources( + domain = 'substance' + ) Error in value[[3L]](cond) : Failed to parse JSON response: cannot open the connection Calls: get_all_sources ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> Execution halted Flavor: r-release-linux-x86_64

Version: 2.1.4
Check: tests
Result: ERROR Running ‘testthat.R’ [9s/32s] 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/RtmpgsyWkT/aspirin.json' The file has been saved to '/home/hornik/tmp/scratch/RtmpgsyWkT/aspirin.json' The file has been saved to '/home/hornik/tmp/scratch/RtmpgsyWkT/aspirin.json' The file has been saved to '/home/hornik/tmp/scratch/RtmpgsyWkT/aspirin.json' The file has been saved to '/home/hornik/tmp/scratch/RtmpgsyWkT/aspirin.sdf' Error in value[[3L]](cond) : Failed to parse JSON response: cannot open the connection Error in value[[3L]](cond) : Failed to parse JSON response: cannot open the connection SDF file saved successfully: File Name: 'aspirin_20250726_065348.sdf' Saved at: /home/hornik/tmp/scratch/RtmpgsyWkT SDF file saved successfully: File Name: 'file.sdf' Saved at: /home/hornik/tmp/scratch/RtmpgsyWkT 'path' is not specified. Saving files into a temporary folder. SDF file saved successfully: File Name: 'file.sdf' Saved at: /home/hornik/tmp/scratch/RtmpgsyWkT Failed to retrieve synonyms for identifier 'aspirin': cannot open the connection Failed to retrieve synonyms for identifier 'ibuprofen': cannot open the connection Failed to retrieve synonyms for identifier 'aspirin': cannot open the connection Failed to retrieve synonyms for identifier '2244': cannot open the connection Failed to retrieve synonyms for identifier 'dncr': cannot open the connection [ FAIL 59 | WARN 14 | SKIP 0 | PASS 92 ] ══ 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-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 ── Failure ('test-get_all_sources.R:20:3'): get all sources for 'assay' ──────── inherits(tmp, "try-error") is not FALSE `actual`: TRUE `expected`: FALSE ── Failure ('test-get_all_sources.R:21:3'): get all sources for 'assay' ──────── all(...) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-get_assays.R:12:3'): pulling assays via an unknown 'namespace' ── allSuccess(tmp) is not FALSE `actual`: TRUE `expected`: FALSE ── Failure ('test-get_assays.R:21:3'): instance() returns an object of class 'PubChemInstance' ── "PubChemInstance" %in% class(instance(assay)) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-get_assays.R:22:3'): instance() returns an object of class 'PubChemInstance' ── `print$instance\(assay$\)` does not match "An object of class 'PubChemInstance'". Actual value: "NULL" Backtrace: ▆ 1. └─testthat::expect_output(print(instance(assay)), "An object of class 'PubChemInstance'") at test-get_assays.R:22:3 2. └─testthat::expect_match(...) 3. └─testthat:::expect_match_(...) ── Error ('test-get_assays.R:26:3'): retrieve() returns selected slots as expected for an assay ── Error in `retrieve.PubChemInstanceList(assay, .slot = "aid", .which = "1234", .to.data.frame = TRUE)`: All instances in the object contain NULL results. Please check if the data was retrieved correctly. Backtrace: ▆ 1. ├─testthat::expect_identical(...) at test-get_assays.R:26:3 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. ├─PubChemR::retrieve(assay, .slot = "aid", .which = "1234", .to.data.frame = TRUE) 5. └─PubChemR:::retrieve.PubChemInstanceList(...) ── Error ('test-get_assays.R:50:3'): retrieve() returns error when unknown/undefined slots or identifiers are provided. ── Error in `retrieve.PubChemInstanceList(assay, .which = "1234")`: All instances in the object contain NULL results. Please check if the data was retrieved correctly. Backtrace: ▆ 1. ├─testthat::expect_warning(retrieve(assay, .which = "1234")) at test-get_assays.R:50:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. ├─PubChemR::retrieve(assay, .which = "1234") 8. └─PubChemR:::retrieve.PubChemInstanceList(assay, .which = "1234") ── Error ('test-get_assays.R:61:3'): checking the effect of '.verbose' argument in retrieve() function ── Error in `retrieve.PubChemInstanceList(assay, .slot = "comment", .verbose = TRUE)`: All instances in the object contain NULL results. Please check if the data was retrieved correctly. Backtrace: ▆ 1. ├─testthat::expect_output(retrieve(assay, .slot = "comment", .verbose = TRUE)) at test-get_assays.R:61:3 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::retrieve(assay, .slot = "comment", .verbose = TRUE) 11. └─PubChemR:::retrieve.PubChemInstanceList(...) ── Failure ('test-get_cids.R:24:5'): CIDs succesfully returns 'data.frame' and 'list' ── { ... } is not TRUE `actual`: FALSE `expected`: TRUE Backtrace: ▆ 1. └─PubChemR (local) toDataFrame(object) at test-get_cids.R:24:5 2. └─testthat::expect_true(...) at test-get_cids.R:12:3 ── Failure ('test-get_cids.R:24:5'): CIDs succesfully returns 'data.frame' and 'list' ── { ... } is not TRUE `actual`: FALSE `expected`: TRUE Backtrace: ▆ 1. └─PubChemR (local) toDataFrame(object) at test-get_cids.R:24:5 2. └─testthat::expect_true(...) at test-get_cids.R:12:3 ── Failure ('test-get_cids.R:47:3'): pulling cids for multiple identifiers with undefined input. ── cids$result[[1]]$success is not TRUE `actual` is NULL `expected` is a logical vector (TRUE) ── Failure ('test-get_cids.R:48:3'): pulling cids for multiple identifiers with undefined input. ── cids$result[[2]]$success is not FALSE `actual` is NULL `expected` is a logical vector (FALSE) ── Failure ('test-get_cids.R:57:3'): undefined/incorrect identifier returns error ── cids$result[[1]]$success is not FALSE `actual` is NULL `expected` is a logical vector (FALSE) ── Failure ('test-get_cids.R:58:3'): undefined/incorrect identifier returns error ── !is.null(cids$result[[1]]$error) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-get_properties.R:16:3'): instance() returns first item from complete list when .which=FALSE ── request_args(tmp, "identifier") == "2244" is not TRUE `actual`: `expected`: TRUE ── Failure ('test-get_properties.R:24:3'): all requested properties returned successfully. ── all(propNamesRequested %in% propNamesReturned) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-get_properties.R:38:3'): .slot vector of length >1 returns warning and accepts the first element in .slot ── (all(is.data.frame(tmp), nrow(tmp) == 1, ncol(tmp) == 2)) is not TRUE `actual`: FALSE `expected`: TRUE ── Error ('test-get_properties.R:44:3'): .which is ignored when '.combine.all = TRUE' ── Error in `retrieve.PubChemInstanceList(props, .combine.all = TRUE, .which = "1234")`: All instances in the object contain NULL results. Please check if the data was retrieved correctly. Backtrace: ▆ 1. ├─testthat::expect_identical(...) at test-get_properties.R:44:3 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. ├─PubChemR::retrieve(props, .combine.all = TRUE, .which = "1234") 5. └─PubChemR:::retrieve.PubChemInstanceList(...) ── Failure ('test-get_properties.R:61:3'): pulling compounds via an unknown 'namespace' ── allSuccess(tmp) is not FALSE `actual`: TRUE `expected`: FALSE ── Failure ('test-get_properties.R:70:3'): instance() returns an object of class 'PubChemInstance' ── "PubChemInstance" %in% class(instance(props)) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-get_properties.R:71:3'): instance() returns an object of class 'PubChemInstance' ── `print$instance\(props$\)` does not match "An object of class 'PubChemInstance'". Actual value: "NULL" Backtrace: ▆ 1. └─testthat::expect_output(print(instance(props)), "An object of class 'PubChemInstance'") at test-get_properties.R:71:3 2. └─testthat::expect_match(...) 3. └─testthat:::expect_match_(...) ── Error ('test-get_properties.R:75:3'): retrieve() returns selected slots as expected for a compound ── Error in `retrieve.PubChemInstanceList(props, .slot = "MolecularWeight", .which = "1234", .to.data.frame = TRUE)`: All instances in the object contain NULL results. Please check if the data was retrieved correctly. Backtrace: ▆ 1. ├─testthat::expect_identical(...) at test-get_properties.R:75:3 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. ├─PubChemR::retrieve(...) 5. └─PubChemR:::retrieve.PubChemInstanceList(...) ── Error ('test-get_properties.R:89:3'): retrieve() returns error when unknown/undefined slots or identifiers are provided. ── Error in `retrieve.PubChemInstanceList(props, .which = "1234", .slot = "unkown_slot")`: All instances in the object contain NULL results. Please check if the data was retrieved correctly. Backtrace: ▆ 1. ├─testthat::expect_null(retrieve(props, .which = "1234", .slot = "unkown_slot")) at test-get_properties.R:89:3 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. ├─PubChemR::retrieve(props, .which = "1234", .slot = "unkown_slot") 5. └─PubChemR:::retrieve.PubChemInstanceList(...) ── Failure ('test-get_pug_rest.R:3:3'): pubChemData() works properly ─────────── is.array(pubChemData(tmp)) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-get_pug_rest.R:19:3'): retry the request and return error ──── tmp$success is not FALSE `actual`: TRUE `expected`: FALSE ── Failure ('test-get_pug_rest.R:36:3'): tests for SDF output successful ─────── { ... } is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-get_pug_rest.R:50:3'): test for PNG output successful ──────── all(tmp$success, is.array(tmp$result)) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-get_pug_rest.R:51:3'): test for PNG output successful ──────── all(tmp2$success, is.array(tmp$result)) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-get_pug_rest.R:53:3'): test for PNG output successful ──────── { ... } is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-get_pug_rest.R:66:3'): test for CSV output successful ──────── { ... } is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-get_pug_rest.R:105:3'): test for JSON output successful ────── { ... } is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-get_pug_view.R:11:3'): multiple identifiers are not allowed. ── tmp$success is not TRUE `actual`: FALSE `expected`: TRUE ── Error ('test-get_pug_view.R:36:3'): sectionList() returns a tibble with number of rows equal to the number of setions ── Error in `UseMethod("sectionList")`: no applicable method for 'sectionList' applied to an object of class "NULL" Backtrace: ▆ 1. ├─PubChemR::sectionList(pview2) at test-get_pug_view.R:36:3 2. └─PubChemR:::sectionList.PugViewInstance(pview2) 3. ├─base::do.call("sectionList", call_args) 4. └─PubChemR::sectionList(object = NULL) ── Error ('test-get_pug_view.R:44:5'): extracting specific section lists form complete list. ── Error in `UseMethod("sectionList")`: no applicable method for 'sectionList' applied to an object of class "NULL" Backtrace: ▆ 1. ├─testthat::expect_true(...) at test-get_pug_view.R:43:3 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. ├─PubChemR::sectionList(...) at test-get_pug_view.R:44:5 5. └─PubChemR:::sectionList.PugViewInstance(...) 6. ├─base::do.call("sectionList", call_args) 7. └─PubChemR::sectionList(object = NULL, .pattern = `<chr>`, .match_type = "contain") ── Error ('test-get_pug_view.R:54:3'): a series of tests on sectionList() ────── Error in `UseMethod("section")`: no applicable method for 'section' applied to an object of class "NULL" Backtrace: ▆ 1. ├─PubChemR::section(pview2) at test-get_pug_view.R:54:3 2. └─PubChemR:::section.PugViewInstance(pview2) 3. ├─base::do.call("section", call_args) 4. └─PubChemR::section(object = NULL, .id = "S1", .verbose = FALSE) ── Error ('test-get_pug_view.R:73:3'): print sections in a nested way ────────── Error in `UseMethod("section")`: no applicable method for 'section' applied to an object of class "NULL" Backtrace: ▆ 1. ├─testthat::expect_output(...) at test-get_pug_view.R:73:3 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::section(section(pview2, .verbose = TRUE), .verbose = TRUE) 11. ├─PubChemR::section(pview2, .verbose = TRUE) 12. └─PubChemR:::section.PugViewInstance(pview2, .verbose = TRUE) 13. ├─base::do.call("section", call_args) 14. └─PubChemR::section(object = NULL, .id = "S1", .verbose = TRUE) ── Failure ('test-get_sdf.R:47:3'): no SDF file saved for unknown/incorrect identifiers ── `tmp` is not NULL `actual` is a character vector ('/home/hornik/tmp/scratch/RtmpgsyWkT/file.sdf') `expected` is NULL ── 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 59 | WARN 14 | SKIP 0 | PASS 92 ] Error: Test failures Execution halted Flavor: r-release-linux-x86_64

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 Quitting from Enhancing_Chemical_Data_Access_with_PubChemR.Rmd:107-109 [unnamed-chunk-9] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `UseMethod()`: ! no applicable method for 'sectionList' applied to an object of class "NULL" --- Backtrace: ▆ 1. └─PubChemR::sectionList(section) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 Quitting from Working_with_PubChemR_to_Access_Chemical_Data.Rmd:882-884 [get_properties_aspirin] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `retrieve.PubChemInstanceList()`: ! All instances in the object contain NULL results. Please check if the data was retrieved correctly. --- Backtrace: ▆ 1. ├─PubChemR::retrieve(object = props, .which = "aspirin", .to.data.frame = TRUE) 2. └─PubChemR:::retrieve.PubChemInstanceList(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'Working_with_PubChemR_to_Access_Chemical_Data.Rmd' failed with diagnostics: All instances in the object contain NULL results. Please check if the data was retrieved correctly. --- failed re-building ‘Working_with_PubChemR_to_Access_Chemical_Data.Rmd’ SUMMARY: processing the following files failed: ‘Enhancing_Chemical_Data_Access_with_PubChemR.Rmd’ ‘Working_with_PubChemR_to_Access_Chemical_Data.Rmd’ Error: Vignette re-building failed. Execution halted Flavor: r-release-linux-x86_64

Version: 2.1.4
Check: examples
Result: ERROR Running examples in 'PubChemR-Ex.R' failed The error most likely occurred in: > ### Name: get_all_sources > ### Title: Retrieve All Sources from PubChem > ### Aliases: get_all_sources > > ### ** Examples > > get_all_sources( + domain = 'substance' + ) Error in value[[3L]](cond) : Failed to parse JSON response: cannot open the connection Calls: get_all_sources ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> Execution halted Flavor: r-release-windows-x86_64

Version: 2.1.4
Check: tests
Result: ERROR Running 'testthat.R' [23s] 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_07_26_01_50_00_9596\Rtmps1RfyN/aspirin.json' The file has been saved to 'D:\temp\2025_07_26_01_50_00_9596\Rtmps1RfyN/aspirin.json' The file has been saved to 'D:\temp\2025_07_26_01_50_00_9596\Rtmps1RfyN/aspirin.json' The file has been saved to 'D:\temp\2025_07_26_01_50_00_9596\Rtmps1RfyN/aspirin.json' The file has been saved to 'D:\temp\2025_07_26_01_50_00_9596\Rtmps1RfyN/aspirin.sdf' Error in value[[3L]](cond) : Failed to parse JSON response: cannot open the connection Error in value[[3L]](cond) : Failed to parse JSON response: cannot open the connection SDF file saved successfully: File Name: 'aspirin_20250726_072646.sdf' Saved at: D:\temp\2025_07_26_01_50_00_9596\Rtmps1RfyN SDF file saved successfully: File Name: 'file.sdf' Saved at: D:\temp\2025_07_26_01_50_00_9596\Rtmps1RfyN 'path' is not specified. Saving files into a temporary folder. SDF file saved successfully: File Name: 'file.sdf' Saved at: D:\temp\2025_07_26_01_50_00_9596\Rtmps1RfyN Failed to retrieve synonyms for identifier 'aspirin': cannot open the connection Failed to retrieve synonyms for identifier 'ibuprofen': cannot open the connection Failed to retrieve synonyms for identifier 'aspirin': cannot open the connection Failed to retrieve synonyms for identifier '2244': cannot open the connection Failed to retrieve synonyms for identifier 'dncr': cannot open the connection [ FAIL 59 | WARN 14 | SKIP 0 | PASS 92 ] ══ 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-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 ── Failure ('test-get_all_sources.R:20:3'): get all sources for 'assay' ──────── inherits(tmp, "try-error") is not FALSE `actual`: TRUE `expected`: FALSE ── Failure ('test-get_all_sources.R:21:3'): get all sources for 'assay' ──────── all(...) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-get_assays.R:12:3'): pulling assays via an unknown 'namespace' ── allSuccess(tmp) is not FALSE `actual`: TRUE `expected`: FALSE ── Failure ('test-get_assays.R:21:3'): instance() returns an object of class 'PubChemInstance' ── "PubChemInstance" %in% class(instance(assay)) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-get_assays.R:22:3'): instance() returns an object of class 'PubChemInstance' ── `print$instance\(assay$\)` does not match "An object of class 'PubChemInstance'". Actual value: "NULL" Backtrace: ▆ 1. └─testthat::expect_output(print(instance(assay)), "An object of class 'PubChemInstance'") at test-get_assays.R:22:3 2. └─testthat::expect_match(...) 3. └─testthat:::expect_match_(...) ── Error ('test-get_assays.R:26:3'): retrieve() returns selected slots as expected for an assay ── Error in `retrieve.PubChemInstanceList(assay, .slot = "aid", .which = "1234", .to.data.frame = TRUE)`: All instances in the object contain NULL results. Please check if the data was retrieved correctly. Backtrace: ▆ 1. ├─testthat::expect_identical(...) at test-get_assays.R:26:3 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. ├─PubChemR::retrieve(assay, .slot = "aid", .which = "1234", .to.data.frame = TRUE) 5. └─PubChemR:::retrieve.PubChemInstanceList(...) ── Error ('test-get_assays.R:50:3'): retrieve() returns error when unknown/undefined slots or identifiers are provided. ── Error in `retrieve.PubChemInstanceList(assay, .which = "1234")`: All instances in the object contain NULL results. Please check if the data was retrieved correctly. Backtrace: ▆ 1. ├─testthat::expect_warning(retrieve(assay, .which = "1234")) at test-get_assays.R:50:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. ├─PubChemR::retrieve(assay, .which = "1234") 8. └─PubChemR:::retrieve.PubChemInstanceList(assay, .which = "1234") ── Error ('test-get_assays.R:61:3'): checking the effect of '.verbose' argument in retrieve() function ── Error in `retrieve.PubChemInstanceList(assay, .slot = "comment", .verbose = TRUE)`: All instances in the object contain NULL results. Please check if the data was retrieved correctly. Backtrace: ▆ 1. ├─testthat::expect_output(retrieve(assay, .slot = "comment", .verbose = TRUE)) at test-get_assays.R:61:3 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::retrieve(assay, .slot = "comment", .verbose = TRUE) 11. └─PubChemR:::retrieve.PubChemInstanceList(...) ── Failure ('test-get_cids.R:24:5'): CIDs succesfully returns 'data.frame' and 'list' ── { ... } is not TRUE `actual`: FALSE `expected`: TRUE Backtrace: ▆ 1. └─PubChemR (local) toDataFrame(object) at test-get_cids.R:24:5 2. └─testthat::expect_true(...) at test-get_cids.R:12:3 ── Failure ('test-get_cids.R:24:5'): CIDs succesfully returns 'data.frame' and 'list' ── { ... } is not TRUE `actual`: FALSE `expected`: TRUE Backtrace: ▆ 1. └─PubChemR (local) toDataFrame(object) at test-get_cids.R:24:5 2. └─testthat::expect_true(...) at test-get_cids.R:12:3 ── Failure ('test-get_cids.R:47:3'): pulling cids for multiple identifiers with undefined input. ── cids$result[[1]]$success is not TRUE `actual` is NULL `expected` is a logical vector (TRUE) ── Failure ('test-get_cids.R:48:3'): pulling cids for multiple identifiers with undefined input. ── cids$result[[2]]$success is not FALSE `actual` is NULL `expected` is a logical vector (FALSE) ── Failure ('test-get_cids.R:57:3'): undefined/incorrect identifier returns error ── cids$result[[1]]$success is not FALSE `actual` is NULL `expected` is a logical vector (FALSE) ── Failure ('test-get_cids.R:58:3'): undefined/incorrect identifier returns error ── !is.null(cids$result[[1]]$error) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-get_properties.R:16:3'): instance() returns first item from complete list when .which=FALSE ── request_args(tmp, "identifier") == "2244" is not TRUE `actual`: `expected`: TRUE ── Failure ('test-get_properties.R:24:3'): all requested properties returned successfully. ── all(propNamesRequested %in% propNamesReturned) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-get_properties.R:38:3'): .slot vector of length >1 returns warning and accepts the first element in .slot ── (all(is.data.frame(tmp), nrow(tmp) == 1, ncol(tmp) == 2)) is not TRUE `actual`: FALSE `expected`: TRUE ── Error ('test-get_properties.R:44:3'): .which is ignored when '.combine.all = TRUE' ── Error in `retrieve.PubChemInstanceList(props, .combine.all = TRUE, .which = "1234")`: All instances in the object contain NULL results. Please check if the data was retrieved correctly. Backtrace: ▆ 1. ├─testthat::expect_identical(...) at test-get_properties.R:44:3 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. ├─PubChemR::retrieve(props, .combine.all = TRUE, .which = "1234") 5. └─PubChemR:::retrieve.PubChemInstanceList(...) ── Failure ('test-get_properties.R:61:3'): pulling compounds via an unknown 'namespace' ── allSuccess(tmp) is not FALSE `actual`: TRUE `expected`: FALSE ── Failure ('test-get_properties.R:70:3'): instance() returns an object of class 'PubChemInstance' ── "PubChemInstance" %in% class(instance(props)) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-get_properties.R:71:3'): instance() returns an object of class 'PubChemInstance' ── `print$instance\(props$\)` does not match "An object of class 'PubChemInstance'". Actual value: "NULL" Backtrace: ▆ 1. └─testthat::expect_output(print(instance(props)), "An object of class 'PubChemInstance'") at test-get_properties.R:71:3 2. └─testthat::expect_match(...) 3. └─testthat:::expect_match_(...) ── Error ('test-get_properties.R:75:3'): retrieve() returns selected slots as expected for a compound ── Error in `retrieve.PubChemInstanceList(props, .slot = "MolecularWeight", .which = "1234", .to.data.frame = TRUE)`: All instances in the object contain NULL results. Please check if the data was retrieved correctly. Backtrace: ▆ 1. ├─testthat::expect_identical(...) at test-get_properties.R:75:3 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. ├─PubChemR::retrieve(...) 5. └─PubChemR:::retrieve.PubChemInstanceList(...) ── Error ('test-get_properties.R:89:3'): retrieve() returns error when unknown/undefined slots or identifiers are provided. ── Error in `retrieve.PubChemInstanceList(props, .which = "1234", .slot = "unkown_slot")`: All instances in the object contain NULL results. Please check if the data was retrieved correctly. Backtrace: ▆ 1. ├─testthat::expect_null(retrieve(props, .which = "1234", .slot = "unkown_slot")) at test-get_properties.R:89:3 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. ├─PubChemR::retrieve(props, .which = "1234", .slot = "unkown_slot") 5. └─PubChemR:::retrieve.PubChemInstanceList(...) ── Failure ('test-get_pug_rest.R:3:3'): pubChemData() works properly ─────────── is.array(pubChemData(tmp)) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-get_pug_rest.R:19:3'): retry the request and return error ──── tmp$success is not FALSE `actual`: TRUE `expected`: FALSE ── Failure ('test-get_pug_rest.R:36:3'): tests for SDF output successful ─────── { ... } is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-get_pug_rest.R:50:3'): test for PNG output successful ──────── all(tmp$success, is.array(tmp$result)) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-get_pug_rest.R:51:3'): test for PNG output successful ──────── all(tmp2$success, is.array(tmp$result)) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-get_pug_rest.R:53:3'): test for PNG output successful ──────── { ... } is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-get_pug_rest.R:66:3'): test for CSV output successful ──────── { ... } is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-get_pug_rest.R:105:3'): test for JSON output successful ────── { ... } is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-get_pug_view.R:11:3'): multiple identifiers are not allowed. ── tmp$success is not TRUE `actual`: FALSE `expected`: TRUE ── Error ('test-get_pug_view.R:36:3'): sectionList() returns a tibble with number of rows equal to the number of setions ── Error in `UseMethod("sectionList")`: no applicable method for 'sectionList' applied to an object of class "NULL" Backtrace: ▆ 1. ├─PubChemR::sectionList(pview2) at test-get_pug_view.R:36:3 2. └─PubChemR:::sectionList.PugViewInstance(pview2) 3. ├─base::do.call("sectionList", call_args) 4. └─PubChemR::sectionList(object = NULL) ── Error ('test-get_pug_view.R:44:5'): extracting specific section lists form complete list. ── Error in `UseMethod("sectionList")`: no applicable method for 'sectionList' applied to an object of class "NULL" Backtrace: ▆ 1. ├─testthat::expect_true(...) at test-get_pug_view.R:43:3 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. ├─PubChemR::sectionList(...) at test-get_pug_view.R:44:5 5. └─PubChemR:::sectionList.PugViewInstance(...) 6. ├─base::do.call("sectionList", call_args) 7. └─PubChemR::sectionList(object = NULL, .pattern = `<chr>`, .match_type = "contain") ── Error ('test-get_pug_view.R:54:3'): a series of tests on sectionList() ────── Error in `UseMethod("section")`: no applicable method for 'section' applied to an object of class "NULL" Backtrace: ▆ 1. ├─PubChemR::section(pview2) at test-get_pug_view.R:54:3 2. └─PubChemR:::section.PugViewInstance(pview2) 3. ├─base::do.call("section", call_args) 4. └─PubChemR::section(object = NULL, .id = "S1", .verbose = FALSE) ── Error ('test-get_pug_view.R:73:3'): print sections in a nested way ────────── Error in `UseMethod("section")`: no applicable method for 'section' applied to an object of class "NULL" Backtrace: ▆ 1. ├─testthat::expect_output(...) at test-get_pug_view.R:73:3 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::section(section(pview2, .verbose = TRUE), .verbose = TRUE) 11. ├─PubChemR::section(pview2, .verbose = TRUE) 12. └─PubChemR:::section.PugViewInstance(pview2, .verbose = TRUE) 13. ├─base::do.call("section", call_args) 14. └─PubChemR::section(object = NULL, .id = "S1", .verbose = TRUE) ── Failure ('test-get_sdf.R:47:3'): no SDF file saved for unknown/incorrect identifiers ── `tmp` is not NULL `actual` is a character vector ('D:\\temp\\2025_07_26_01_50_00_9596\\Rtmps1RfyN/file.sdf') `expected` is NULL ── 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 59 | WARN 14 | SKIP 0 | PASS 92 ] Error: Test failures Execution halted Flavor: r-release-windows-x86_64

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 Quitting from Enhancing_Chemical_Data_Access_with_PubChemR.Rmd:107-109 [unnamed-chunk-9] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `UseMethod()`: ! no applicable method for 'sectionList' applied to an object of class "NULL" --- Backtrace: ▆ 1. └─PubChemR::sectionList(section) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 Quitting from Working_with_PubChemR_to_Access_Chemical_Data.Rmd:882-884 [get_properties_aspirin] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `retrieve.PubChemInstanceList()`: ! All instances in the object contain NULL results. Please check if the data was retrieved correctly. --- Backtrace: ▆ 1. ├─PubChemR::retrieve(object = props, .which = "aspirin", .to.data.frame = TRUE) 2. └─PubChemR:::retrieve.PubChemInstanceList(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'Working_with_PubChemR_to_Access_Chemical_Data.Rmd' failed with diagnostics: All instances in the object contain NULL results. Please check if the data was retrieved correctly. --- failed re-building 'Working_with_PubChemR_to_Access_Chemical_Data.Rmd' SUMMARY: processing the following files failed: 'Enhancing_Chemical_Data_Access_with_PubChemR.Rmd' 'Working_with_PubChemR_to_Access_Chemical_Data.Rmd' Error: Vignette re-building failed. Execution halted Flavor: r-release-windows-x86_64