CRAN Package Check Results for Package PubChemR

Last updated on 2025-04-26 20:50:41 CEST.

Flavor	Version	Tinstall	Tcheck	Ttotal	Status	Flags
r-devel-linux-x86_64-debian-clang	2.1.4	8.81	178.59	187.40	OK
r-devel-linux-x86_64-debian-gcc	2.1.4	5.01	116.92	121.93	OK
r-devel-linux-x86_64-fedora-clang	2.1.4			295.12	OK
r-devel-linux-x86_64-fedora-gcc	2.1.4			294.17	OK
r-devel-windows-x86_64	2.1.4	10.00	373.00	383.00	ERROR
r-patched-linux-x86_64	2.1.4	8.51	170.60	179.11	OK
r-release-linux-x86_64	2.1.4	8.01	169.53	177.54	OK
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	1089.00	1100.00	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	13.00	1064.00	1077.00	ERROR

Check Details

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 --- finished 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:1038-1048 [download_jsson] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `curl::curl_fetch_memory()`: ! Could not connect to server [pubchem.ncbi.nlm.nih.gov]: Failed to connect to pubchem.ncbi.nlm.nih.gov port 443 after 9929 ms: Could not connect to server --- Backtrace: ▆ 1. ├─PubChemR::download(...) 2. │ └─PubChemR:::get_pubchem(...) 3. │ └─httr::GET(...) 4. │ └─httr:::request_perform(req, hu$handle$handle) 5. │ ├─httr:::request_fetch(req$output, req$url, handle) 6. │ └─httr:::request_fetch.write_memory(req$output, req$url, handle) 7. │ └─curl::curl_fetch_memory(url, handle = handle) 8. └─curl:::raise_libcurl_error(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'Working_with_PubChemR_to_Access_Chemical_Data.Rmd' failed with diagnostics: Could not connect to server [pubchem.ncbi.nlm.nih.gov]: Failed to connect to pubchem.ncbi.nlm.nih.gov port 443 after 9929 ms: Could not connect to server --- failed re-building 'Working_with_PubChemR_to_Access_Chemical_Data.Rmd' SUMMARY: processing the following file failed: 'Working_with_PubChemR_to_Access_Chemical_Data.Rmd' Error: Vignette re-building failed. Execution halted Flavor: r-devel-windows-x86_64

Version: 2.1.4
Check: examples
Result: ERROR Running examples in 'PubChemR-Ex.R' failed The error most likely occurred in: > ### 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 get_pubchem(identifier, namespace, domain, operation, outformat, : c(Code = "PUGREST.ServerBusy", Message = "Too many requests or server too busy") Calls: download -> get_pubchem Execution halted Flavors: r-release-windows-x86_64, r-oldrel-windows-x86_64

Version: 2.1.4
Check: tests
Result: ERROR Running 'testthat.R' [479s] 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 get_pubchem(identifier, namespace, domain, operation, outformat, : c(Code = "PUGREST.Timeout", Message = "Request timed out") Error in get_pubchem(identifier, namespace, domain, operation, outformat, : c(Code = "PUGREST.ServerBusy", Message = "Too many requests or server too busy") Error in get_pubchem(identifier, namespace, domain, operation, outformat, : c(Code = "PUGREST.ServerBusy", Message = "Too many requests or server too busy") Error in get_pubchem(identifier, namespace, domain, operation, outformat, : c(Code = "PUGREST.ServerBusy", Message = "Too many requests or server too busy") Error in file(con, "r") : cannot open the connection Error in value[[3L]](cond) : Failed to retrieve sources for the specified domain: c(Code = "PUGREST.ServerBusy", Message = "Too many requests or server too busy") Error in value[[3L]](cond) : Failed to retrieve sources for the specified domain: c(Code = "PUGREST.ServerBusy", Message = "Too many requests or server too busy") Request failed [503]. Retrying in 3.1 seconds... Request failed [503]. Retrying in 4.2 seconds... Request failed [503]. Retrying in 1.3 seconds... Request failed [400]. Retrying in 4.7 seconds... Request failed [504]. Retrying in 1 seconds... Request failed [504]. Retrying in 5.1 seconds... Request failed [504]. Retrying in 2 seconds... Request failed [504]. Retrying in 5.2 seconds... Request failed [503]. Retrying in 2.9 seconds... Error: Received no content to write to the SDF file. URL may be invalid or the content is missing. Error: Received no content to write to the SDF file. URL may be invalid or the content is missing. 'path' is not specified. Saving files into a temporary folder. Error: Received no content to write to the SDF file. URL may be invalid or the content is missing. [ FAIL 35 | WARN 34 | SKIP 0 | PASS 135 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── 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_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:5:1'): pulling via 'aid' is succesfull ────────── allSuccess(object) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-get_assays.R:42:3'): retrieve() returns selected slots as expected for an assay ── { ... } is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-get_cids.R:20:5'): pulling cids via 'name' is succesfull ───── allSuccess(object) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-get_cids.R:20:5'): pulling cids via 'smiles' is succesfull ─── allSuccess(object) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-get_cids.R:47:3'): pulling cids for multiple identifiers with undefined input. ── cids$result[[1]]$success is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-get_properties.R:12:1'): pulling via 'cid' is succesfull ───── allSuccess(object) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-get_properties.R:24:3'): all requested properties returned successfully. ── all(propNamesRequested %in% propNamesReturned) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-get_properties.R:38:3'): .slot vector of length >1 returns warning and accepts the first element in .slot ── (all(is.data.frame(tmp), nrow(tmp) == 1, ncol(tmp) == 2)) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-get_pug_rest.R:3:3'): pubChemData() works properly ─────────── is.array(pubChemData(tmp)) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-get_pug_rest.R:28:3'): tests for SDF output successful ─────── { ... } is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-get_pug_rest.R:32:3'): tests for SDF output successful ─────── all(is.list(pubChemData(tmp)), length(pubChemData(tmp)) == 0) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-get_pug_rest.R:50:3'): test for PNG output successful ──────── all(tmp$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$result)) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-get_pug_rest.R:53:3'): test for PNG output successful ──────── { ... } is not TRUE `actual`: `expected`: TRUE ── Error ('test-get_sdf.R:14:3'): pulling SDFs via 'name' is succesful ───────── Error in `file.exists(tmp)`: invalid 'file' argument Backtrace: ▆ 1. ├─testthat::expect_true(file.exists(tmp)) at test-get_sdf.R:14:3 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─base::file.exists(tmp) ── Failure ('test-get_sdf.R:30:3'): pulling SDFs via 'cid' is succesful ──────── file.exists(file.path(temp_dir, "file.sdf")) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-get_sdf.R:60:3'): save SDF files to temporary working directory when path is not specified. ── file.exists(file.path(default_path, "file.sdf")) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-get_sids.R:20:5'): pulling sids via 'name' is succesfull ───── allSuccess(object) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-get_sids.R:20:5'): pulling sids via 'cid' is succesfull ────── allSuccess(object) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-get_sids.R:53:3'): pulling sids for multiple identifiers with undefined input. ── sids$result[[1]]$success is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-get_substances.R:6:1'): pulling via 'name' is succesfull ───── allSuccess(object) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-get_substances.R:30:3'): incorrect/undefined substance identifier returns error ── all(!is.null(tmp$result[[1]]$error), is.list(tmp$result[[1]]$error)) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-get_substances.R:35:3'): '.verbose' works as expected ──────── retrieve(...) returns visibly, not invisibly. ── Failure ('test-get_substances.R:38:3'): '.verbose' works as expected ──────── retrieve(...) returns visibly, not invisibly. ── 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:6:1'): pulling via 'name' is succesfull ─────── allSuccess(object) is not TRUE `actual`: FALSE `expected`: TRUE ── 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:41:3'): pulling synonyms via 'name' is succesful ── allSuccess(tmp) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-get_synonyms.R:50:3'): pulling synonyms via 'cid' is succesful ── allSuccess(tmp) is not TRUE `actual`: FALSE `expected`: TRUE [ FAIL 35 | WARN 34 | SKIP 0 | PASS 135 ] 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 --- finished 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:955-961 [get_all_sources_substance] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `value[[3L]]()`: ! Failed to retrieve sources for the specified domain: c(Code = "PUGREST.ServerBusy", Message = "Too many requests or server too busy") --- Backtrace: ▆ 1. └─PubChemR::get_all_sources(domain = "substance") 2. └─base::tryCatch(...) 3. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 5. └─value[[3L]](cond) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'Working_with_PubChemR_to_Access_Chemical_Data.Rmd' failed with diagnostics: Failed to retrieve sources for the specified domain: c(Code = "PUGREST.ServerBusy", Message = "Too many requests or server too busy") --- failed re-building 'Working_with_PubChemR_to_Access_Chemical_Data.Rmd' SUMMARY: processing the following file failed: 'Working_with_PubChemR_to_Access_Chemical_Data.Rmd' Error: Vignette re-building failed. Execution halted Flavors: r-release-windows-x86_64, r-oldrel-windows-x86_64

Version: 2.1.4
Check: tests
Result: ERROR Running 'testthat.R' [254s] 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 get_pubchem(identifier, namespace, domain, operation, outformat, : c(Code = "PUGREST.ServerBusy", Message = "Too many requests or server too busy") Error in get_pubchem(identifier, namespace, domain, operation, outformat, : c(Code = "PUGREST.ServerBusy", Message = "Too many requests or server too busy") Error in get_pubchem(identifier, namespace, domain, operation, outformat, : c(Code = "PUGREST.ServerBusy", Message = "Too many requests or server too busy") Error in get_pubchem(identifier, namespace, domain, operation, outformat, : c(Code = "PUGREST.ServerBusy", Message = "Too many requests or server too busy") Error in file(con, "r") : cannot open the connection Request failed [503]. Retrying in 2.9 seconds... Request failed [503]. Retrying in 7.5 seconds... Request failed [503]. Retrying in 1 seconds... Request failed [503]. Retrying in 6.4 seconds... Request failed [400]. Retrying in 3.2 seconds... Request failed [503]. Retrying in 1 seconds... Request failed [503]. Retrying in 2.7 seconds... Request failed [504]. Retrying in 7.6 seconds... Request failed [504]. Retrying in 2.1 seconds... Request failed [504]. Retrying in 4.5 seconds... Request failed [503]. Retrying in 1 seconds... Request failed [503]. Retrying in 1 seconds... Request failed [503]. Retrying in 1 seconds... Error: Received no content to write to the SDF file. URL may be invalid or the content is missing. Error: Received no content to write to the SDF file. URL may be invalid or the content is missing. 'path' is not specified. Saving files into a temporary folder. Error: Received no content to write to the SDF file. URL may be invalid or the content is missing. [ FAIL 35 | WARN 47 | SKIP 0 | PASS 135 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── 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_assays.R:5:1'): pulling via 'aid' is succesfull ────────── allSuccess(object) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-get_assays.R:42:3'): retrieve() returns selected slots as expected for an assay ── { ... } is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-get_assays.R:61:3'): checking the effect of '.verbose' argument in retrieve() function ── `retrieve(assay, .slot = "comment", .verbose = TRUE)` produced no output ── Failure ('test-get_assays.R:62:3'): checking the effect of '.verbose' argument in retrieve() function ── retrieve(assay, .slot = "comment", .verbose = TRUE, .combine.all = TRUE) returns visibly, not invisibly. ── Failure ('test-get_cids.R:20:5'): pulling cids via 'name' is succesfull ───── allSuccess(object) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-get_cids.R:20:5'): pulling cids via 'smiles' is succesfull ─── allSuccess(object) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-get_cids.R:47:3'): pulling cids for multiple identifiers with undefined input. ── cids$result[[1]]$success is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-get_properties.R:12:1'): pulling via 'cid' is succesfull ───── allSuccess(object) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-get_properties.R:24:3'): all requested properties returned successfully. ── all(propNamesRequested %in% propNamesReturned) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-get_properties.R:38:3'): .slot vector of length >1 returns warning and accepts the first element in .slot ── (all(is.data.frame(tmp), nrow(tmp) == 1, ncol(tmp) == 2)) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-get_pug_rest.R:3:3'): pubChemData() works properly ─────────── is.array(pubChemData(tmp)) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-get_pug_rest.R:28:3'): tests for SDF output successful ─────── { ... } is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-get_pug_rest.R:32:3'): tests for SDF output successful ─────── all(is.list(pubChemData(tmp)), length(pubChemData(tmp)) == 0) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-get_pug_rest.R:35:3'): tests for SDF output successful ─────── file.exists(file.path(tmp2$fileDetails$Path, tmp2$fileDetails$Name)) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-get_pug_rest.R:50:3'): test for PNG output successful ──────── all(tmp$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$result)) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-get_pug_rest.R:53:3'): test for PNG output successful ──────── { ... } is not TRUE `actual`: `expected`: TRUE ── Error ('test-get_sdf.R:14:3'): pulling SDFs via 'name' is succesful ───────── Error in `file.exists(tmp)`: invalid 'file' argument Backtrace: ▆ 1. ├─testthat::expect_true(file.exists(tmp)) at test-get_sdf.R:14:3 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─base::file.exists(tmp) ── Failure ('test-get_sdf.R:30:3'): pulling SDFs via 'cid' is succesful ──────── file.exists(file.path(temp_dir, "file.sdf")) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-get_sdf.R:60:3'): save SDF files to temporary working directory when path is not specified. ── file.exists(file.path(default_path, "file.sdf")) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-get_sids.R:20:5'): pulling sids via 'name' is succesfull ───── allSuccess(object) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-get_sids.R:20:5'): pulling sids via 'cid' is succesfull ────── allSuccess(object) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-get_sids.R:20:5'): pulling sids via 'smiles' is succesfull ─── allSuccess(object) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-get_sids.R:53:3'): pulling sids for multiple identifiers with undefined input. ── sids$result[[1]]$success is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-get_substances.R:6:1'): pulling via 'name' is succesfull ───── allSuccess(object) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-get_substances.R:30:3'): incorrect/undefined substance identifier returns error ── all(!is.null(tmp$result[[1]]$error), is.list(tmp$result[[1]]$error)) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-get_substances.R:35:3'): '.verbose' works as expected ──────── retrieve(...) returns visibly, not invisibly. ── Failure ('test-get_substances.R:38:3'): '.verbose' works as expected ──────── retrieve(...) returns visibly, not invisibly. ── 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:6:1'): pulling via 'name' is succesfull ─────── allSuccess(object) is not TRUE `actual`: FALSE `expected`: TRUE ── 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:41:3'): pulling synonyms via 'name' is succesful ── allSuccess(tmp) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-get_synonyms.R:50:3'): pulling synonyms via 'cid' is succesful ── allSuccess(tmp) is not TRUE `actual`: FALSE `expected`: TRUE [ FAIL 35 | WARN 47 | SKIP 0 | PASS 135 ] Error: Test failures Execution halted Flavor: r-oldrel-windows-x86_64