• using R version 4.5.1 (2025-06-13)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-14 (Debian 14.2.0-19) 14.2.0     GNU Fortran (Debian 14.2.0-19) 14.2.0
• running under: Debian GNU/Linux 13 (trixie)
• using session charset: UTF-8
• checking for file ‘PubChemR/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘PubChemR’ version ‘2.1.4’
• 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/2s] OK
• checking whether the namespace can be loaded with stated dependencies ... [1s/2s] 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/15s] 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 ... [2s/6s] 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
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [9s/33s] 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
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [24s/58s] 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
• checking PDF version of manual ... [5s/8s] OK
• checking HTML version of manual ... [1s/3s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 3 ERRORs