CRAN Package Check Results for Package fqar

Last updated on 2024-10-05 03:49:23 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.5.3 7.51 64.64 72.15 ERROR
r-devel-linux-x86_64-debian-gcc 0.5.3 5.24 46.34 51.58 ERROR
r-devel-linux-x86_64-fedora-clang 0.5.3 114.94 OK
r-devel-linux-x86_64-fedora-gcc 0.5.3 119.53 OK
r-devel-windows-x86_64 0.5.3 13.00 109.00 122.00 ERROR
r-patched-linux-x86_64 0.5.3 7.37 62.55 69.92 OK
r-release-linux-x86_64 0.5.3 6.77 60.85 67.62 ERROR
r-release-macos-arm64 0.5.3 74.00 OK
r-release-macos-x86_64 0.5.3 141.00 OK
r-release-windows-x86_64 0.5.3 11.00 108.00 119.00 ERROR
r-oldrel-macos-arm64 0.5.3 77.00 OK
r-oldrel-macos-x86_64 0.5.3 126.00 OK
r-oldrel-windows-x86_64 0.5.3 15.00 119.00 134.00 ERROR

Check Details

Version: 0.5.3
Check: examples
Result: ERROR Running examples in ‘fqar-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: species_acronym > ### Title: Acronym of a species in a specified database > ### Aliases: species_acronym > > ### ** Examples > > species_acronym("Anemone canadensis", database_id = 149) Error: parse error: unallowed token at this point in JSON text tatus" : "success", "data" : } (right here) ------^ Execution halted Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-release-linux-x86_64

Version: 0.5.3
Check: tests
Result: ERROR Running ‘testthat.R’ [11s/33s] 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/tests.html > # * https://testthat.r-lib.org/reference/test_package.html#special-files > > library(testthat) > library(fqar) > > test_check("fqar") data_set must be a dataframe obtained from the universalFQA.org website. Type ?download_transect for help. data_set must be a dataframe obtained from the universalFQA.org website. Type ?download_transect for help. [ FAIL 2 | WARN 0 | SKIP 0 | PASS 363 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-download_database.R:10:3'): download_database works ──────────── Error in `(function (database_id) { if (!is.numeric(database_id)) { stop("database_id must be an integer.", call. = FALSE) } if (database_id%%1 != 0) { stop("database_id must be an integer.", call. = FALSE) } empty <- data.frame(V1 = character(0), V2 = character(0), V3 = character(0), V4 = character(0), V5 = character(0), V6 = character(0), V7 = character(0), V8 = character(0), V9 = character(0)) class(empty) <- c("tbl_df", "tbl", "data.frame") if (database_id == -40000) { return(invisible(empty)) } database_address <- paste0("http://universalfqa.org/get/database/", database_id) ua <- httr::user_agent("https://github.com/equitable-equations/fqar") database_get <- tryCatch(httr::GET(database_address, ua, timeout(2)), error = function(e) { message("No response from universalFQA.org. Please check internet connection.") character(0) }) cl <- class(database_get) if (cl != "response") { return(invisible(empty)) } if (httr::http_error(database_get)) { message(paste("API request to universalFQA.org failed. Error", httr::status_code(assessments_get))) return(invisible(empty)) } database_text <- httr::content(database_get, "text", encoding = "ISO-8859-1") database_json <- jsonlite::fromJSON(database_text) list_data <- database_json[[2]] if ((list_data[[1]] == "The requested assessment is not public") & (!is.na(list_data[[1]]))) { message("The requested assessment is not public.") return(invisible(empty)) } max_length <- max(unlist(lapply(list_data, length))) list_data <- lapply(list_data, function(x) { length(x) <- max_length unlist(x) }) db_out <- as.data.frame(do.call(rbind, list_data)) if (db_out[5, 2] == 0) { message("Specified database is empty.") } class(db_out) <- c("tbl_df", "tbl", "data.frame") db_out })(database_id = database_id)`: object 'assessments_get' not found Backtrace: ▆ 1. ├─testthat::expect_message(download_database(3)) at test-download_database.R:10:3 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. └─fqar::download_database(3) 8. ├─fqar:::download_database_internal(database_id) 9. │ ├─base::withVisible(eval(mc, parent.frame())) 10. │ └─base::eval(mc, parent.frame()) 11. │ └─base::eval(mc, parent.frame()) 12. └─fqar (local) `<fn>`(database_id = database_id) 13. ├─base::message(...) 14. ├─base::paste(...) 15. └─httr::status_code(assessments_get) ── Error ('test-species_acronym.R:14:3'): species_acronym works ──────────────── Error: parse error: unallowed token at this point in JSON text tatus" : "success", "data" : } (right here) ------^ Backtrace: ▆ 1. ├─base::suppressMessages(download_database(149)) at test-species_acronym.R:14:3 2. │ └─base::withCallingHandlers(...) 3. └─fqar::download_database(149) 4. ├─fqar:::download_database_internal(database_id) 5. │ ├─base::withVisible(eval(mc, parent.frame())) 6. │ └─base::eval(mc, parent.frame()) 7. │ └─base::eval(mc, parent.frame()) 8. └─fqar (local) `<fn>`(database_id = database_id) 9. └─jsonlite::fromJSON(database_text) 10. └─jsonlite:::parse_and_simplify(...) 11. └─jsonlite:::parseJSON(txt, bigint_as_char) 12. └─jsonlite:::parse_string(txt, bigint_as_char) [ FAIL 2 | WARN 0 | SKIP 0 | PASS 363 ] Error: Test failures Execution halted Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.5.3
Check: tests
Result: ERROR Running ‘testthat.R’ [7s/28s] 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/tests.html > # * https://testthat.r-lib.org/reference/test_package.html#special-files > > library(testthat) > library(fqar) > > test_check("fqar") data_set must be a dataframe obtained from the universalFQA.org website. Type ?download_transect for help. data_set must be a dataframe obtained from the universalFQA.org website. Type ?download_transect for help. [ FAIL 2 | WARN 0 | SKIP 0 | PASS 363 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-download_database.R:10:3'): download_database works ──────────── Error in `(function (database_id) { if (!is.numeric(database_id)) { stop("database_id must be an integer.", call. = FALSE) } if (database_id%%1 != 0) { stop("database_id must be an integer.", call. = FALSE) } empty <- data.frame(V1 = character(0), V2 = character(0), V3 = character(0), V4 = character(0), V5 = character(0), V6 = character(0), V7 = character(0), V8 = character(0), V9 = character(0)) class(empty) <- c("tbl_df", "tbl", "data.frame") if (database_id == -40000) { return(invisible(empty)) } database_address <- paste0("http://universalfqa.org/get/database/", database_id) ua <- httr::user_agent("https://github.com/equitable-equations/fqar") database_get <- tryCatch(httr::GET(database_address, ua, timeout(2)), error = function(e) { message("No response from universalFQA.org. Please check internet connection.") character(0) }) cl <- class(database_get) if (cl != "response") { return(invisible(empty)) } if (httr::http_error(database_get)) { message(paste("API request to universalFQA.org failed. Error", httr::status_code(assessments_get))) return(invisible(empty)) } database_text <- httr::content(database_get, "text", encoding = "ISO-8859-1") database_json <- jsonlite::fromJSON(database_text) list_data <- database_json[[2]] if ((list_data[[1]] == "The requested assessment is not public") & (!is.na(list_data[[1]]))) { message("The requested assessment is not public.") return(invisible(empty)) } max_length <- max(unlist(lapply(list_data, length))) list_data <- lapply(list_data, function(x) { length(x) <- max_length unlist(x) }) db_out <- as.data.frame(do.call(rbind, list_data)) if (db_out[5, 2] == 0) { message("Specified database is empty.") } class(db_out) <- c("tbl_df", "tbl", "data.frame") db_out })(database_id = database_id)`: object 'assessments_get' not found Backtrace: ▆ 1. ├─testthat::expect_message(download_database(3)) at test-download_database.R:10:3 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. └─fqar::download_database(3) 8. ├─fqar:::download_database_internal(database_id) 9. │ ├─base::withVisible(eval(mc, parent.frame())) 10. │ └─base::eval(mc, parent.frame()) 11. │ └─base::eval(mc, parent.frame()) 12. └─fqar (local) `<fn>`(database_id = database_id) 13. ├─base::message(...) 14. ├─base::paste(...) 15. └─httr::status_code(assessments_get) ── Error ('test-species_acronym.R:14:3'): species_acronym works ──────────────── Error: parse error: unallowed token at this point in JSON text tatus" : "success", "data" : } (right here) ------^ Backtrace: ▆ 1. ├─base::suppressMessages(download_database(149)) at test-species_acronym.R:14:3 2. │ └─base::withCallingHandlers(...) 3. └─fqar::download_database(149) 4. ├─fqar:::download_database_internal(database_id) 5. │ ├─base::withVisible(eval(mc, parent.frame())) 6. │ └─base::eval(mc, parent.frame()) 7. │ └─base::eval(mc, parent.frame()) 8. └─fqar (local) `<fn>`(database_id = database_id) 9. └─jsonlite::fromJSON(database_text) 10. └─jsonlite:::parse_and_simplify(...) 11. └─jsonlite:::parseJSON(txt, bigint_as_char) 12. └─jsonlite:::parse_string(txt, bigint_as_char) [ FAIL 2 | WARN 0 | SKIP 0 | PASS 363 ] Error: Test failures Execution halted Flavor: r-devel-linux-x86_64-debian-gcc

Version: 0.5.3
Check: examples
Result: ERROR Running examples in 'fqar-Ex.R' failed The error most likely occurred in: > ### Name: database_glance > ### Title: Obtain tidy summary information for a floristic quality database > ### Aliases: database_glance > > ### ** Examples > > # While database_glance can be used with a .csv file downloaded manually > # from the universal FQA website, it is most typically used in combination > # with download_database(). > > chicago_db <- download_database(database_id = 1) Error in (function (database_id) : object 'assessments_get' not found Calls: download_database ... eval -> <Anonymous> -> message -> paste -> <Anonymous> Execution halted Flavor: r-devel-windows-x86_64

Version: 0.5.3
Check: tests
Result: ERROR Running 'testthat.R' [30s] 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/tests.html > # * https://testthat.r-lib.org/reference/test_package.html#special-files > > library(testthat) > library(fqar) > > test_check("fqar") [ FAIL 24 | WARN 0 | SKIP 0 | PASS 231 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-database_glance.R:17:3'): database_glance works ──────────────── Error in `(function (database_id) { if (!is.numeric(database_id)) { stop("database_id must be an integer.", call. = FALSE) } if (database_id%%1 != 0) { stop("database_id must be an integer.", call. = FALSE) } empty <- data.frame(V1 = character(0), V2 = character(0), V3 = character(0), V4 = character(0), V5 = character(0), V6 = character(0), V7 = character(0), V8 = character(0), V9 = character(0)) class(empty) <- c("tbl_df", "tbl", "data.frame") if (database_id == -40000) { return(invisible(empty)) } database_address <- paste0("http://universalfqa.org/get/database/", database_id) ua <- httr::user_agent("https://github.com/equitable-equations/fqar") database_get <- tryCatch(httr::GET(database_address, ua, timeout(2)), error = function(e) { message("No response from universalFQA.org. Please check internet connection.") character(0) }) cl <- class(database_get) if (cl != "response") { return(invisible(empty)) } if (httr::http_error(database_get)) { message(paste("API request to universalFQA.org failed. Error", httr::status_code(assessments_get))) return(invisible(empty)) } database_text <- httr::content(database_get, "text", encoding = "ISO-8859-1") database_json <- jsonlite::fromJSON(database_text) list_data <- database_json[[2]] if ((list_data[[1]] == "The requested assessment is not public") & (!is.na(list_data[[1]]))) { message("The requested assessment is not public.") return(invisible(empty)) } max_length <- max(unlist(lapply(list_data, length))) list_data <- lapply(list_data, function(x) { length(x) <- max_length unlist(x) }) db_out <- as.data.frame(do.call(rbind, list_data)) if (db_out[5, 2] == 0) { message("Specified database is empty.") } class(db_out) <- c("tbl_df", "tbl", "data.frame") db_out })(database_id = database_id)`: object 'assessments_get' not found Backtrace: ▆ 1. ├─base::suppressMessages(download_database(1)) at test-database_glance.R:17:3 2. │ └─base::withCallingHandlers(...) 3. └─fqar::download_database(1) 4. ├─fqar:::download_database_internal(database_id) 5. │ ├─base::withVisible(eval(mc, parent.frame())) 6. │ └─base::eval(mc, parent.frame()) 7. │ └─base::eval(mc, parent.frame()) 8. └─fqar (local) `<fn>`(database_id = database_id) 9. ├─base::message(...) 10. ├─base::paste(...) 11. └─httr::status_code(assessments_get) ── Error ('test-download_database.R:10:3'): download_database works ──────────── Error in `(function (database_id) { if (!is.numeric(database_id)) { stop("database_id must be an integer.", call. = FALSE) } if (database_id%%1 != 0) { stop("database_id must be an integer.", call. = FALSE) } empty <- data.frame(V1 = character(0), V2 = character(0), V3 = character(0), V4 = character(0), V5 = character(0), V6 = character(0), V7 = character(0), V8 = character(0), V9 = character(0)) class(empty) <- c("tbl_df", "tbl", "data.frame") if (database_id == -40000) { return(invisible(empty)) } database_address <- paste0("http://universalfqa.org/get/database/", database_id) ua <- httr::user_agent("https://github.com/equitable-equations/fqar") database_get <- tryCatch(httr::GET(database_address, ua, timeout(2)), error = function(e) { message("No response from universalFQA.org. Please check internet connection.") character(0) }) cl <- class(database_get) if (cl != "response") { return(invisible(empty)) } if (httr::http_error(database_get)) { message(paste("API request to universalFQA.org failed. Error", httr::status_code(assessments_get))) return(invisible(empty)) } database_text <- httr::content(database_get, "text", encoding = "ISO-8859-1") database_json <- jsonlite::fromJSON(database_text) list_data <- database_json[[2]] if ((list_data[[1]] == "The requested assessment is not public") & (!is.na(list_data[[1]]))) { message("The requested assessment is not public.") return(invisible(empty)) } max_length <- max(unlist(lapply(list_data, length))) list_data <- lapply(list_data, function(x) { length(x) <- max_length unlist(x) }) db_out <- as.data.frame(do.call(rbind, list_data)) if (db_out[5, 2] == 0) { message("Specified database is empty.") } class(db_out) <- c("tbl_df", "tbl", "data.frame") db_out })(database_id = database_id)`: object 'assessments_get' not found Backtrace: ▆ 1. ├─testthat::expect_message(download_database(3)) at test-download_database.R:10:3 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. └─fqar::download_database(3) 8. ├─fqar:::download_database_internal(database_id) 9. │ ├─base::withVisible(eval(mc, parent.frame())) 10. │ └─base::eval(mc, parent.frame()) 11. │ └─base::eval(mc, parent.frame()) 12. └─fqar (local) `<fn>`(database_id = database_id) 13. ├─base::message(...) 14. ├─base::paste(...) 15. └─httr::status_code(assessments_get) ── Error ('test-download_database_internal.R:10:3'): download_database_internal works ── Error in `(function (database_id) { if (!is.numeric(database_id)) { stop("database_id must be an integer.", call. = FALSE) } if (database_id%%1 != 0) { stop("database_id must be an integer.", call. = FALSE) } empty <- data.frame(V1 = character(0), V2 = character(0), V3 = character(0), V4 = character(0), V5 = character(0), V6 = character(0), V7 = character(0), V8 = character(0), V9 = character(0)) class(empty) <- c("tbl_df", "tbl", "data.frame") if (database_id == -40000) { return(invisible(empty)) } database_address <- paste0("http://universalfqa.org/get/database/", database_id) ua <- httr::user_agent("https://github.com/equitable-equations/fqar") database_get <- tryCatch(httr::GET(database_address, ua, timeout(2)), error = function(e) { message("No response from universalFQA.org. Please check internet connection.") character(0) }) cl <- class(database_get) if (cl != "response") { return(invisible(empty)) } if (httr::http_error(database_get)) { message(paste("API request to universalFQA.org failed. Error", httr::status_code(assessments_get))) return(invisible(empty)) } database_text <- httr::content(database_get, "text", encoding = "ISO-8859-1") database_json <- jsonlite::fromJSON(database_text) list_data <- database_json[[2]] if ((list_data[[1]] == "The requested assessment is not public") & (!is.na(list_data[[1]]))) { message("The requested assessment is not public.") return(invisible(empty)) } max_length <- max(unlist(lapply(list_data, length))) list_data <- lapply(list_data, function(x) { length(x) <- max_length unlist(x) }) db_out <- as.data.frame(do.call(rbind, list_data)) if (db_out[5, 2] == 0) { message("Specified database is empty.") } class(db_out) <- c("tbl_df", "tbl", "data.frame") db_out })(database_id = 1)`: object 'assessments_get' not found Backtrace: ▆ 1. └─fqar (local) `<fn>`(database_id = 1) 2. ├─base::message(...) 3. ├─base::paste(...) 4. └─httr::status_code(assessments_get) ── Error ('test-download_transect.R:10:3'): download_transect works ──────────── Error in `(function (transect_id) { if (!is.numeric(transect_id)) { stop("transect_id must be an integer.", call. = FALSE) } if (transect_id%%1 != 0) { stop("transect_id must be an integer.", call. = FALSE) } empty <- data.frame(V1 = character(0), V2 = character(0), V3 = character(0), V4 = character(0), V5 = character(0), V6 = character(0), V7 = character(0), V8 = character(0), V9 = character(0), V10 = character(0), V11 = character(0), V12 = character(0), V13 = character(0), V14 = character(0)) class(empty) <- c("tbl_df", "tbl", "data.frame") if (transect_id == -40000) { return(invisible(empty)) } trans_address <- paste0("http://universalfqa.org/get/transect/", transect_id) ua <- httr::user_agent("https://github.com/equitable-equations/fqar") trans_get <- tryCatch(httr::GET(trans_address, ua, timeout(2)), error = function(e) { message("No response from universalFQA.org. Please check internet connection.") character(0) }) cl <- class(trans_get) if (cl != "response") { return(invisible(empty)) } if (httr::http_error(trans_get)) { message(paste("API request to universalFQA.org failed. Error", httr::status_code(assessments_get))) return(invisible(empty)) } trans_text <- httr::content(trans_get, "text", encoding = "ISO-8859-1") trans_json <- jsonlite::fromJSON(trans_text) list_data <- trans_json[[2]] if ((list_data[[1]] == "The requested assessment is not public") & (!is.na(list_data[[1]]))) { message("The requested assessment is not public.") return(invisible(empty)) } max_length <- max(unlist(lapply(list_data, length))) list_data <- lapply(list_data, function(x) { length(x) <- max_length unlist(x) }) out <- as.data.frame(do.call(rbind, list_data)) class(out) <- c("tbl_df", "tbl", "data.frame") out })(transect_id = transect_id)`: object 'assessments_get' not found Backtrace: ▆ 1. ├─base::suppressMessages(download_transect(6322)) at test-download_transect.R:10:3 2. │ └─base::withCallingHandlers(...) 3. └─fqar::download_transect(6322) 4. ├─fqar:::download_transect_internal(transect_id) 5. │ ├─base::withVisible(eval(mc, parent.frame())) 6. │ └─base::eval(mc, parent.frame()) 7. │ └─base::eval(mc, parent.frame()) 8. └─fqar (local) `<fn>`(transect_id = transect_id) 9. ├─base::message(...) 10. ├─base::paste(...) 11. └─httr::status_code(assessments_get) ── Error ('test-download_transect_internal.R:10:3'): download_transect_internal works ── Error in `(function (transect_id) { if (!is.numeric(transect_id)) { stop("transect_id must be an integer.", call. = FALSE) } if (transect_id%%1 != 0) { stop("transect_id must be an integer.", call. = FALSE) } empty <- data.frame(V1 = character(0), V2 = character(0), V3 = character(0), V4 = character(0), V5 = character(0), V6 = character(0), V7 = character(0), V8 = character(0), V9 = character(0), V10 = character(0), V11 = character(0), V12 = character(0), V13 = character(0), V14 = character(0)) class(empty) <- c("tbl_df", "tbl", "data.frame") if (transect_id == -40000) { return(invisible(empty)) } trans_address <- paste0("http://universalfqa.org/get/transect/", transect_id) ua <- httr::user_agent("https://github.com/equitable-equations/fqar") trans_get <- tryCatch(httr::GET(trans_address, ua, timeout(2)), error = function(e) { message("No response from universalFQA.org. Please check internet connection.") character(0) }) cl <- class(trans_get) if (cl != "response") { return(invisible(empty)) } if (httr::http_error(trans_get)) { message(paste("API request to universalFQA.org failed. Error", httr::status_code(assessments_get))) return(invisible(empty)) } trans_text <- httr::content(trans_get, "text", encoding = "ISO-8859-1") trans_json <- jsonlite::fromJSON(trans_text) list_data <- trans_json[[2]] if ((list_data[[1]] == "The requested assessment is not public") & (!is.na(list_data[[1]]))) { message("The requested assessment is not public.") return(invisible(empty)) } max_length <- max(unlist(lapply(list_data, length))) list_data <- lapply(list_data, function(x) { length(x) <- max_length unlist(x) }) out <- as.data.frame(do.call(rbind, list_data)) class(out) <- c("tbl_df", "tbl", "data.frame") out })(transect_id = 6322)`: object 'assessments_get' not found Backtrace: ▆ 1. └─fqar (local) `<fn>`(transect_id = 6322) 2. ├─base::message(...) 3. ├─base::paste(...) 4. └─httr::status_code(assessments_get) ── Error ('test-download_transect_list.R:3:3'): download_transect_list works ─── Error in `(function (database_id) { if (!is.numeric(database_id)) { stop("database_id must be an integer corresponding to an existing FQA database. Use index_fqa_databases() to obtain a data frame of valid options.", call. = FALSE) } if (database_id%%1 != 0) { stop("database_id must be an integer corresponding to an existing FQA database. Use index_fqa_databases() to obtain a data frame of valid options.", call. = FALSE) } empty_df <- data.frame(id = numeric(0), assessment = character(0), date = numeric(0), site = character(0), practitioner = character(0)) class(empty_df) <- c("tbl_df", "tbl", "data.frame") empty_df$date <- as.Date(empty_df$date) if (database_id == -40000) { return(invisible(empty_df)) } trans_address <- paste0("http://universalfqa.org/get/database/", database_id, "/transect") ua <- httr::user_agent("https://github.com/equitable-equations/fqar") trans_get <- tryCatch(httr::GET(trans_address, ua, timeout(2)), error = function(e) { message("No response from universalFQA.org. Please check internet connection.") character(0) }) cl <- class(trans_get) if (cl != "response") { return(invisible(empty_df)) } if (httr::http_error(trans_get)) { message(paste("API request to universalFQA.org failed. Error", httr::status_code(assessments_get))) return(invisible(empty_df)) } trans_text <- httr::content(trans_get, "text", encoding = "ISO-8859-1") trans_json <- jsonlite::fromJSON(trans_text) list_data <- trans_json[[2]] transect_summary <- as.data.frame(list_data) if (nrow(transect_summary) == 0) { message("No data associated with specified database_id.") return(invisible(empty_df)) } colnames(transect_summary) <- c("id", "assessment", "date", "site", "practitioner") transect_summary$id <- as.double(transect_summary$id) transect_summary$date[transect_summary$date == "0000-00-00"] <- NA transect_summary$date <- as.Date(transect_summary$date) class(transect_summary) <- c("tbl_df", "tbl", "data.frame") transect_summary })(database_id = database_id)`: object 'assessments_get' not found Backtrace: ▆ 1. ├─testthat::expect_equal(...) at test-download_transect_list.R:3:3 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. ├─base::suppressMessages(download_transect_list(-2)) 5. │ └─base::withCallingHandlers(...) 6. └─fqar::download_transect_list(-2) 7. └─fqar::index_fqa_transects(database_id) 8. ├─fqar:::index_fqa_transects_internal(database_id) 9. │ ├─base::withVisible(eval(mc, parent.frame())) 10. │ └─base::eval(mc, parent.frame()) 11. │ └─base::eval(mc, parent.frame()) 12. └─fqar (local) `<fn>`(database_id = database_id) 13. ├─base::message(...) 14. ├─base::paste(...) 15. └─httr::status_code(assessments_get) ── Error ('test-index_fqa_databases.R:5:3'): index_fqa_databases works ───────── Error in `(function () { empty_df <- data.frame(database_id = numeric(0), region = character(0), year = numeric(0), description = character(0)) class(empty_df) <- c("tbl_df", "tbl", "data.frame") databases_address <- "http://universalfqa.org/get/database/" ua <- httr::user_agent("https://github.com/equitable-equations/fqar") databases_get <- tryCatch(httr::GET(databases_address, ua, timeout(2)), error = function(e) { message("No response from UniversalFQA.org. Please check internet connection.") character(0) }) cl <- class(databases_get) if (cl != "response") { return(invisible(empty_df)) } if (httr::http_error(databases_get)) { message(paste("API request to universalFQA.org failed. Error", httr::status_code(assessments_get))) return(invisible(empty_df)) } databases_text <- httr::content(databases_get, "text", encoding = "ISO-8859-1") databases_json <- jsonlite::fromJSON(databases_text) list_data <- databases_json[[2]] databases <- as.data.frame(list_data) databases[, c(1, 3)] <- lapply(databases[, c(1, 3)], as.double) colnames(databases) <- c("database_id", "region", "year", "description") class(databases) <- c("tbl_df", "tbl", "data.frame") databases })()`: object 'assessments_get' not found Backtrace: ▆ 1. ├─base::suppressMessages(index_fqa_databases()) at test-index_fqa_databases.R:5:3 2. │ └─base::withCallingHandlers(...) 3. └─fqar::index_fqa_databases() 4. ├─fqar:::index_fqa_databases_internal() 5. │ ├─base::withVisible(eval(mc, parent.frame())) 6. │ └─base::eval(mc, parent.frame()) 7. │ └─base::eval(mc, parent.frame()) 8. └─fqar (local) `<fn>`() 9. ├─base::message(...) 10. ├─base::paste(...) 11. └─httr::status_code(assessments_get) ── Error ('test-index_fqa_databases_internal.R:5:3'): index_fqa_databases_internal works ── Error in `(function () { empty_df <- data.frame(database_id = numeric(0), region = character(0), year = numeric(0), description = character(0)) class(empty_df) <- c("tbl_df", "tbl", "data.frame") databases_address <- "http://universalfqa.org/get/database/" ua <- httr::user_agent("https://github.com/equitable-equations/fqar") databases_get <- tryCatch(httr::GET(databases_address, ua, timeout(2)), error = function(e) { message("No response from UniversalFQA.org. Please check internet connection.") character(0) }) cl <- class(databases_get) if (cl != "response") { return(invisible(empty_df)) } if (httr::http_error(databases_get)) { message(paste("API request to universalFQA.org failed. Error", httr::status_code(assessments_get))) return(invisible(empty_df)) } databases_text <- httr::content(databases_get, "text", encoding = "ISO-8859-1") databases_json <- jsonlite::fromJSON(databases_text) list_data <- databases_json[[2]] databases <- as.data.frame(list_data) databases[, c(1, 3)] <- lapply(databases[, c(1, 3)], as.double) colnames(databases) <- c("database_id", "region", "year", "description") class(databases) <- c("tbl_df", "tbl", "data.frame") databases })()`: object 'assessments_get' not found Backtrace: ▆ 1. └─fqar (local) `<fn>`() 2. ├─base::message(...) 3. ├─base::paste(...) 4. └─httr::status_code(assessments_get) ── Error ('test-index_fqa_transects.R:11:3'): index_fqa_transects works ──────── Error in `(function (database_id) { if (!is.numeric(database_id)) { stop("database_id must be an integer corresponding to an existing FQA database. Use index_fqa_databases() to obtain a data frame of valid options.", call. = FALSE) } if (database_id%%1 != 0) { stop("database_id must be an integer corresponding to an existing FQA database. Use index_fqa_databases() to obtain a data frame of valid options.", call. = FALSE) } empty_df <- data.frame(id = numeric(0), assessment = character(0), date = numeric(0), site = character(0), practitioner = character(0)) class(empty_df) <- c("tbl_df", "tbl", "data.frame") empty_df$date <- as.Date(empty_df$date) if (database_id == -40000) { return(invisible(empty_df)) } trans_address <- paste0("http://universalfqa.org/get/database/", database_id, "/transect") ua <- httr::user_agent("https://github.com/equitable-equations/fqar") trans_get <- tryCatch(httr::GET(trans_address, ua, timeout(2)), error = function(e) { message("No response from universalFQA.org. Please check internet connection.") character(0) }) cl <- class(trans_get) if (cl != "response") { return(invisible(empty_df)) } if (httr::http_error(trans_get)) { message(paste("API request to universalFQA.org failed. Error", httr::status_code(assessments_get))) return(invisible(empty_df)) } trans_text <- httr::content(trans_get, "text", encoding = "ISO-8859-1") trans_json <- jsonlite::fromJSON(trans_text) list_data <- trans_json[[2]] transect_summary <- as.data.frame(list_data) if (nrow(transect_summary) == 0) { message("No data associated with specified database_id.") return(invisible(empty_df)) } colnames(transect_summary) <- c("id", "assessment", "date", "site", "practitioner") transect_summary$id <- as.double(transect_summary$id) transect_summary$date[transect_summary$date == "0000-00-00"] <- NA transect_summary$date <- as.Date(transect_summary$date) class(transect_summary) <- c("tbl_df", "tbl", "data.frame") transect_summary })(database_id = database_id)`: object 'assessments_get' not found Backtrace: ▆ 1. ├─base::suppressMessages(index_fqa_transects(1)) at test-index_fqa_transects.R:11:3 2. │ └─base::withCallingHandlers(...) 3. └─fqar::index_fqa_transects(1) 4. ├─fqar:::index_fqa_transects_internal(database_id) 5. │ ├─base::withVisible(eval(mc, parent.frame())) 6. │ └─base::eval(mc, parent.frame()) 7. │ └─base::eval(mc, parent.frame()) 8. └─fqar (local) `<fn>`(database_id = database_id) 9. ├─base::message(...) 10. ├─base::paste(...) 11. └─httr::status_code(assessments_get) ── Error ('test-index_fqa_transects_internal.R:11:3'): index_fqa_transects_internal works ── Error in `(function (database_id) { if (!is.numeric(database_id)) { stop("database_id must be an integer corresponding to an existing FQA database. Use index_fqa_databases() to obtain a data frame of valid options.", call. = FALSE) } if (database_id%%1 != 0) { stop("database_id must be an integer corresponding to an existing FQA database. Use index_fqa_databases() to obtain a data frame of valid options.", call. = FALSE) } empty_df <- data.frame(id = numeric(0), assessment = character(0), date = numeric(0), site = character(0), practitioner = character(0)) class(empty_df) <- c("tbl_df", "tbl", "data.frame") empty_df$date <- as.Date(empty_df$date) if (database_id == -40000) { return(invisible(empty_df)) } trans_address <- paste0("http://universalfqa.org/get/database/", database_id, "/transect") ua <- httr::user_agent("https://github.com/equitable-equations/fqar") trans_get <- tryCatch(httr::GET(trans_address, ua, timeout(2)), error = function(e) { message("No response from universalFQA.org. Please check internet connection.") character(0) }) cl <- class(trans_get) if (cl != "response") { return(invisible(empty_df)) } if (httr::http_error(trans_get)) { message(paste("API request to universalFQA.org failed. Error", httr::status_code(assessments_get))) return(invisible(empty_df)) } trans_text <- httr::content(trans_get, "text", encoding = "ISO-8859-1") trans_json <- jsonlite::fromJSON(trans_text) list_data <- trans_json[[2]] transect_summary <- as.data.frame(list_data) if (nrow(transect_summary) == 0) { message("No data associated with specified database_id.") return(invisible(empty_df)) } colnames(transect_summary) <- c("id", "assessment", "date", "site", "practitioner") transect_summary$id <- as.double(transect_summary$id) transect_summary$date[transect_summary$date == "0000-00-00"] <- NA transect_summary$date <- as.Date(transect_summary$date) class(transect_summary) <- c("tbl_df", "tbl", "data.frame") transect_summary })(database_id = 1)`: object 'assessments_get' not found Backtrace: ▆ 1. └─fqar (local) `<fn>`(database_id = 1) 2. ├─base::message(...) 3. ├─base::paste(...) 4. └─httr::status_code(assessments_get) ── Error ('test-is_transect.R:10:3'): is_transect works ──────────────────────── Error in `(function (transect_id) { if (!is.numeric(transect_id)) { stop("transect_id must be an integer.", call. = FALSE) } if (transect_id%%1 != 0) { stop("transect_id must be an integer.", call. = FALSE) } empty <- data.frame(V1 = character(0), V2 = character(0), V3 = character(0), V4 = character(0), V5 = character(0), V6 = character(0), V7 = character(0), V8 = character(0), V9 = character(0), V10 = character(0), V11 = character(0), V12 = character(0), V13 = character(0), V14 = character(0)) class(empty) <- c("tbl_df", "tbl", "data.frame") if (transect_id == -40000) { return(invisible(empty)) } trans_address <- paste0("http://universalfqa.org/get/transect/", transect_id) ua <- httr::user_agent("https://github.com/equitable-equations/fqar") trans_get <- tryCatch(httr::GET(trans_address, ua, timeout(2)), error = function(e) { message("No response from universalFQA.org. Please check internet connection.") character(0) }) cl <- class(trans_get) if (cl != "response") { return(invisible(empty)) } if (httr::http_error(trans_get)) { message(paste("API request to universalFQA.org failed. Error", httr::status_code(assessments_get))) return(invisible(empty)) } trans_text <- httr::content(trans_get, "text", encoding = "ISO-8859-1") trans_json <- jsonlite::fromJSON(trans_text) list_data <- trans_json[[2]] if ((list_data[[1]] == "The requested assessment is not public") & (!is.na(list_data[[1]]))) { message("The requested assessment is not public.") return(invisible(empty)) } max_length <- max(unlist(lapply(list_data, length))) list_data <- lapply(list_data, function(x) { length(x) <- max_length unlist(x) }) out <- as.data.frame(do.call(rbind, list_data)) class(out) <- c("tbl_df", "tbl", "data.frame") out })(transect_id = transect_id)`: object 'assessments_get' not found Backtrace: ▆ 1. ├─base::suppressMessages(download_transect(4492)) at test-is_transect.R:10:3 2. │ └─base::withCallingHandlers(...) 3. └─fqar::download_transect(4492) 4. ├─fqar:::download_transect_internal(transect_id) 5. │ ├─base::withVisible(eval(mc, parent.frame())) 6. │ └─base::eval(mc, parent.frame()) 7. │ └─base::eval(mc, parent.frame()) 8. └─fqar (local) `<fn>`(transect_id = transect_id) 9. ├─base::message(...) 10. ├─base::paste(...) 11. └─httr::status_code(assessments_get) ── Error ('test-is_transect_list.R:3:3'): is_transect_list works ─────────────── Error in `(function (transect_id) { if (!is.numeric(transect_id)) { stop("transect_id must be an integer.", call. = FALSE) } if (transect_id%%1 != 0) { stop("transect_id must be an integer.", call. = FALSE) } empty <- data.frame(V1 = character(0), V2 = character(0), V3 = character(0), V4 = character(0), V5 = character(0), V6 = character(0), V7 = character(0), V8 = character(0), V9 = character(0), V10 = character(0), V11 = character(0), V12 = character(0), V13 = character(0), V14 = character(0)) class(empty) <- c("tbl_df", "tbl", "data.frame") if (transect_id == -40000) { return(invisible(empty)) } trans_address <- paste0("http://universalfqa.org/get/transect/", transect_id) ua <- httr::user_agent("https://github.com/equitable-equations/fqar") trans_get <- tryCatch(httr::GET(trans_address, ua, timeout(2)), error = function(e) { message("No response from universalFQA.org. Please check internet connection.") character(0) }) cl <- class(trans_get) if (cl != "response") { return(invisible(empty)) } if (httr::http_error(trans_get)) { message(paste("API request to universalFQA.org failed. Error", httr::status_code(assessments_get))) return(invisible(empty)) } trans_text <- httr::content(trans_get, "text", encoding = "ISO-8859-1") trans_json <- jsonlite::fromJSON(trans_text) list_data <- trans_json[[2]] if ((list_data[[1]] == "The requested assessment is not public") & (!is.na(list_data[[1]]))) { message("The requested assessment is not public.") return(invisible(empty)) } max_length <- max(unlist(lapply(list_data, length))) list_data <- lapply(list_data, function(x) { length(x) <- max_length unlist(x) }) out <- as.data.frame(do.call(rbind, list_data)) class(out) <- c("tbl_df", "tbl", "data.frame") out })(transect_id = transect_id)`: object 'assessments_get' not found Backtrace: ▆ 1. ├─base::suppressMessages(download_transect(4492)) at test-is_transect_list.R:3:3 2. │ └─base::withCallingHandlers(...) 3. └─fqar::download_transect(4492) 4. ├─fqar:::download_transect_internal(transect_id) 5. │ ├─base::withVisible(eval(mc, parent.frame())) 6. │ └─base::eval(mc, parent.frame()) 7. │ └─base::eval(mc, parent.frame()) 8. └─fqar (local) `<fn>`(transect_id = transect_id) 9. ├─base::message(...) 10. ├─base::paste(...) 11. └─httr::status_code(assessments_get) ── Error ('test-species_acronym.R:14:3'): species_acronym works ──────────────── Error in `(function (database_id) { if (!is.numeric(database_id)) { stop("database_id must be an integer.", call. = FALSE) } if (database_id%%1 != 0) { stop("database_id must be an integer.", call. = FALSE) } empty <- data.frame(V1 = character(0), V2 = character(0), V3 = character(0), V4 = character(0), V5 = character(0), V6 = character(0), V7 = character(0), V8 = character(0), V9 = character(0)) class(empty) <- c("tbl_df", "tbl", "data.frame") if (database_id == -40000) { return(invisible(empty)) } database_address <- paste0("http://universalfqa.org/get/database/", database_id) ua <- httr::user_agent("https://github.com/equitable-equations/fqar") database_get <- tryCatch(httr::GET(database_address, ua, timeout(2)), error = function(e) { message("No response from universalFQA.org. Please check internet connection.") character(0) }) cl <- class(database_get) if (cl != "response") { return(invisible(empty)) } if (httr::http_error(database_get)) { message(paste("API request to universalFQA.org failed. Error", httr::status_code(assessments_get))) return(invisible(empty)) } database_text <- httr::content(database_get, "text", encoding = "ISO-8859-1") database_json <- jsonlite::fromJSON(database_text) list_data <- database_json[[2]] if ((list_data[[1]] == "The requested assessment is not public") & (!is.na(list_data[[1]]))) { message("The requested assessment is not public.") return(invisible(empty)) } max_length <- max(unlist(lapply(list_data, length))) list_data <- lapply(list_data, function(x) { length(x) <- max_length unlist(x) }) db_out <- as.data.frame(do.call(rbind, list_data)) if (db_out[5, 2] == 0) { message("Specified database is empty.") } class(db_out) <- c("tbl_df", "tbl", "data.frame") db_out })(database_id = database_id)`: object 'assessments_get' not found Backtrace: ▆ 1. ├─base::suppressMessages(download_database(149)) at test-species_acronym.R:14:3 2. │ └─base::withCallingHandlers(...) 3. └─fqar::download_database(149) 4. ├─fqar:::download_database_internal(database_id) 5. │ ├─base::withVisible(eval(mc, parent.frame())) 6. │ └─base::eval(mc, parent.frame()) 7. │ └─base::eval(mc, parent.frame()) 8. └─fqar (local) `<fn>`(database_id = database_id) 9. ├─base::message(...) 10. ├─base::paste(...) 11. └─httr::status_code(assessments_get) ── Error ('test-species_c.R:17:3'): species_c works ──────────────────────────── Error in `(function (database_id) { if (!is.numeric(database_id)) { stop("database_id must be an integer.", call. = FALSE) } if (database_id%%1 != 0) { stop("database_id must be an integer.", call. = FALSE) } empty <- data.frame(V1 = character(0), V2 = character(0), V3 = character(0), V4 = character(0), V5 = character(0), V6 = character(0), V7 = character(0), V8 = character(0), V9 = character(0)) class(empty) <- c("tbl_df", "tbl", "data.frame") if (database_id == -40000) { return(invisible(empty)) } database_address <- paste0("http://universalfqa.org/get/database/", database_id) ua <- httr::user_agent("https://github.com/equitable-equations/fqar") database_get <- tryCatch(httr::GET(database_address, ua, timeout(2)), error = function(e) { message("No response from universalFQA.org. Please check internet connection.") character(0) }) cl <- class(database_get) if (cl != "response") { return(invisible(empty)) } if (httr::http_error(database_get)) { message(paste("API request to universalFQA.org failed. Error", httr::status_code(assessments_get))) return(invisible(empty)) } database_text <- httr::content(database_get, "text", encoding = "ISO-8859-1") database_json <- jsonlite::fromJSON(database_text) list_data <- database_json[[2]] if ((list_data[[1]] == "The requested assessment is not public") & (!is.na(list_data[[1]]))) { message("The requested assessment is not public.") return(invisible(empty)) } max_length <- max(unlist(lapply(list_data, length))) list_data <- lapply(list_data, function(x) { length(x) <- max_length unlist(x) }) db_out <- as.data.frame(do.call(rbind, list_data)) if (db_out[5, 2] == 0) { message("Specified database is empty.") } class(db_out) <- c("tbl_df", "tbl", "data.frame") db_out })(database_id = database_id)`: object 'assessments_get' not found Backtrace: ▆ 1. ├─base::suppressMessages(download_database(1)) at test-species_c.R:17:3 2. │ └─base::withCallingHandlers(...) 3. └─fqar::download_database(1) 4. ├─fqar:::download_database_internal(database_id) 5. │ ├─base::withVisible(eval(mc, parent.frame())) 6. │ └─base::eval(mc, parent.frame()) 7. │ └─base::eval(mc, parent.frame()) 8. └─fqar (local) `<fn>`(database_id = database_id) 9. ├─base::message(...) 10. ├─base::paste(...) 11. └─httr::status_code(assessments_get) ── Error ('test-species_common_name.R:14:3'): species_common_name works ──────── Error in `(function (database_id) { if (!is.numeric(database_id)) { stop("database_id must be an integer.", call. = FALSE) } if (database_id%%1 != 0) { stop("database_id must be an integer.", call. = FALSE) } empty <- data.frame(V1 = character(0), V2 = character(0), V3 = character(0), V4 = character(0), V5 = character(0), V6 = character(0), V7 = character(0), V8 = character(0), V9 = character(0)) class(empty) <- c("tbl_df", "tbl", "data.frame") if (database_id == -40000) { return(invisible(empty)) } database_address <- paste0("http://universalfqa.org/get/database/", database_id) ua <- httr::user_agent("https://github.com/equitable-equations/fqar") database_get <- tryCatch(httr::GET(database_address, ua, timeout(2)), error = function(e) { message("No response from universalFQA.org. Please check internet connection.") character(0) }) cl <- class(database_get) if (cl != "response") { return(invisible(empty)) } if (httr::http_error(database_get)) { message(paste("API request to universalFQA.org failed. Error", httr::status_code(assessments_get))) return(invisible(empty)) } database_text <- httr::content(database_get, "text", encoding = "ISO-8859-1") database_json <- jsonlite::fromJSON(database_text) list_data <- database_json[[2]] if ((list_data[[1]] == "The requested assessment is not public") & (!is.na(list_data[[1]]))) { message("The requested assessment is not public.") return(invisible(empty)) } max_length <- max(unlist(lapply(list_data, length))) list_data <- lapply(list_data, function(x) { length(x) <- max_length unlist(x) }) db_out <- as.data.frame(do.call(rbind, list_data)) if (db_out[5, 2] == 0) { message("Specified database is empty.") } class(db_out) <- c("tbl_df", "tbl", "data.frame") db_out })(database_id = database_id)`: object 'assessments_get' not found Backtrace: ▆ 1. ├─base::suppressMessages(download_database(1)) at test-species_common_name.R:14:3 2. │ └─base::withCallingHandlers(...) 3. └─fqar::download_database(1) 4. ├─fqar:::download_database_internal(database_id) 5. │ ├─base::withVisible(eval(mc, parent.frame())) 6. │ └─base::eval(mc, parent.frame()) 7. │ └─base::eval(mc, parent.frame()) 8. └─fqar (local) `<fn>`(database_id = database_id) 9. ├─base::message(...) 10. ├─base::paste(...) 11. └─httr::status_code(assessments_get) ── Error ('test-species_nativity.R:14:3'): species_nativity works ────────────── Error in `(function (database_id) { if (!is.numeric(database_id)) { stop("database_id must be an integer.", call. = FALSE) } if (database_id%%1 != 0) { stop("database_id must be an integer.", call. = FALSE) } empty <- data.frame(V1 = character(0), V2 = character(0), V3 = character(0), V4 = character(0), V5 = character(0), V6 = character(0), V7 = character(0), V8 = character(0), V9 = character(0)) class(empty) <- c("tbl_df", "tbl", "data.frame") if (database_id == -40000) { return(invisible(empty)) } database_address <- paste0("http://universalfqa.org/get/database/", database_id) ua <- httr::user_agent("https://github.com/equitable-equations/fqar") database_get <- tryCatch(httr::GET(database_address, ua, timeout(2)), error = function(e) { message("No response from universalFQA.org. Please check internet connection.") character(0) }) cl <- class(database_get) if (cl != "response") { return(invisible(empty)) } if (httr::http_error(database_get)) { message(paste("API request to universalFQA.org failed. Error", httr::status_code(assessments_get))) return(invisible(empty)) } database_text <- httr::content(database_get, "text", encoding = "ISO-8859-1") database_json <- jsonlite::fromJSON(database_text) list_data <- database_json[[2]] if ((list_data[[1]] == "The requested assessment is not public") & (!is.na(list_data[[1]]))) { message("The requested assessment is not public.") return(invisible(empty)) } max_length <- max(unlist(lapply(list_data, length))) list_data <- lapply(list_data, function(x) { length(x) <- max_length unlist(x) }) db_out <- as.data.frame(do.call(rbind, list_data)) if (db_out[5, 2] == 0) { message("Specified database is empty.") } class(db_out) <- c("tbl_df", "tbl", "data.frame") db_out })(database_id = database_id)`: object 'assessments_get' not found Backtrace: ▆ 1. ├─base::suppressMessages(download_database(1)) at test-species_nativity.R:14:3 2. │ └─base::withCallingHandlers(...) 3. └─fqar::download_database(1) 4. ├─fqar:::download_database_internal(database_id) 5. │ ├─base::withVisible(eval(mc, parent.frame())) 6. │ └─base::eval(mc, parent.frame()) 7. │ └─base::eval(mc, parent.frame()) 8. └─fqar (local) `<fn>`(database_id = database_id) 9. ├─base::message(...) 10. ├─base::paste(...) 11. └─httr::status_code(assessments_get) ── Error ('test-species_phys.R:15:3'): species_phys works ────────────────────── Error in `(function (database_id) { if (!is.numeric(database_id)) { stop("database_id must be an integer.", call. = FALSE) } if (database_id%%1 != 0) { stop("database_id must be an integer.", call. = FALSE) } empty <- data.frame(V1 = character(0), V2 = character(0), V3 = character(0), V4 = character(0), V5 = character(0), V6 = character(0), V7 = character(0), V8 = character(0), V9 = character(0)) class(empty) <- c("tbl_df", "tbl", "data.frame") if (database_id == -40000) { return(invisible(empty)) } database_address <- paste0("http://universalfqa.org/get/database/", database_id) ua <- httr::user_agent("https://github.com/equitable-equations/fqar") database_get <- tryCatch(httr::GET(database_address, ua, timeout(2)), error = function(e) { message("No response from universalFQA.org. Please check internet connection.") character(0) }) cl <- class(database_get) if (cl != "response") { return(invisible(empty)) } if (httr::http_error(database_get)) { message(paste("API request to universalFQA.org failed. Error", httr::status_code(assessments_get))) return(invisible(empty)) } database_text <- httr::content(database_get, "text", encoding = "ISO-8859-1") database_json <- jsonlite::fromJSON(database_text) list_data <- database_json[[2]] if ((list_data[[1]] == "The requested assessment is not public") & (!is.na(list_data[[1]]))) { message("The requested assessment is not public.") return(invisible(empty)) } max_length <- max(unlist(lapply(list_data, length))) list_data <- lapply(list_data, function(x) { length(x) <- max_length unlist(x) }) db_out <- as.data.frame(do.call(rbind, list_data)) if (db_out[5, 2] == 0) { message("Specified database is empty.") } class(db_out) <- c("tbl_df", "tbl", "data.frame") db_out })(database_id = database_id)`: object 'assessments_get' not found Backtrace: ▆ 1. ├─base::suppressMessages(download_database(1)) at test-species_phys.R:15:3 2. │ └─base::withCallingHandlers(...) 3. └─fqar::download_database(1) 4. ├─fqar:::download_database_internal(database_id) 5. │ ├─base::withVisible(eval(mc, parent.frame())) 6. │ └─base::eval(mc, parent.frame()) 7. │ └─base::eval(mc, parent.frame()) 8. └─fqar (local) `<fn>`(database_id = database_id) 9. ├─base::message(...) 10. ├─base::paste(...) 11. └─httr::status_code(assessments_get) ── Error ('test-species_w.R:13:3'): species_w works ──────────────────────────── Error in `(function (database_id) { if (!is.numeric(database_id)) { stop("database_id must be an integer.", call. = FALSE) } if (database_id%%1 != 0) { stop("database_id must be an integer.", call. = FALSE) } empty <- data.frame(V1 = character(0), V2 = character(0), V3 = character(0), V4 = character(0), V5 = character(0), V6 = character(0), V7 = character(0), V8 = character(0), V9 = character(0)) class(empty) <- c("tbl_df", "tbl", "data.frame") if (database_id == -40000) { return(invisible(empty)) } database_address <- paste0("http://universalfqa.org/get/database/", database_id) ua <- httr::user_agent("https://github.com/equitable-equations/fqar") database_get <- tryCatch(httr::GET(database_address, ua, timeout(2)), error = function(e) { message("No response from universalFQA.org. Please check internet connection.") character(0) }) cl <- class(database_get) if (cl != "response") { return(invisible(empty)) } if (httr::http_error(database_get)) { message(paste("API request to universalFQA.org failed. Error", httr::status_code(assessments_get))) return(invisible(empty)) } database_text <- httr::content(database_get, "text", encoding = "ISO-8859-1") database_json <- jsonlite::fromJSON(database_text) list_data <- database_json[[2]] if ((list_data[[1]] == "The requested assessment is not public") & (!is.na(list_data[[1]]))) { message("The requested assessment is not public.") return(invisible(empty)) } max_length <- max(unlist(lapply(list_data, length))) list_data <- lapply(list_data, function(x) { length(x) <- max_length unlist(x) }) db_out <- as.data.frame(do.call(rbind, list_data)) if (db_out[5, 2] == 0) { message("Specified database is empty.") } class(db_out) <- c("tbl_df", "tbl", "data.frame") db_out })(database_id = database_id)`: object 'assessments_get' not found Backtrace: ▆ 1. ├─base::suppressMessages(download_database(1)) at test-species_w.R:13:3 2. │ └─base::withCallingHandlers(...) 3. └─fqar::download_database(1) 4. ├─fqar:::download_database_internal(database_id) 5. │ ├─base::withVisible(eval(mc, parent.frame())) 6. │ └─base::eval(mc, parent.frame()) 7. │ └─base::eval(mc, parent.frame()) 8. └─fqar (local) `<fn>`(database_id = database_id) 9. ├─base::message(...) 10. ├─base::paste(...) 11. └─httr::status_code(assessments_get) ── Error ('test-transect_glance.R:16:3'): transect_glance works ──────────────── Error in `(function (transect_id) { if (!is.numeric(transect_id)) { stop("transect_id must be an integer.", call. = FALSE) } if (transect_id%%1 != 0) { stop("transect_id must be an integer.", call. = FALSE) } empty <- data.frame(V1 = character(0), V2 = character(0), V3 = character(0), V4 = character(0), V5 = character(0), V6 = character(0), V7 = character(0), V8 = character(0), V9 = character(0), V10 = character(0), V11 = character(0), V12 = character(0), V13 = character(0), V14 = character(0)) class(empty) <- c("tbl_df", "tbl", "data.frame") if (transect_id == -40000) { return(invisible(empty)) } trans_address <- paste0("http://universalfqa.org/get/transect/", transect_id) ua <- httr::user_agent("https://github.com/equitable-equations/fqar") trans_get <- tryCatch(httr::GET(trans_address, ua, timeout(2)), error = function(e) { message("No response from universalFQA.org. Please check internet connection.") character(0) }) cl <- class(trans_get) if (cl != "response") { return(invisible(empty)) } if (httr::http_error(trans_get)) { message(paste("API request to universalFQA.org failed. Error", httr::status_code(assessments_get))) return(invisible(empty)) } trans_text <- httr::content(trans_get, "text", encoding = "ISO-8859-1") trans_json <- jsonlite::fromJSON(trans_text) list_data <- trans_json[[2]] if ((list_data[[1]] == "The requested assessment is not public") & (!is.na(list_data[[1]]))) { message("The requested assessment is not public.") return(invisible(empty)) } max_length <- max(unlist(lapply(list_data, length))) list_data <- lapply(list_data, function(x) { length(x) <- max_length unlist(x) }) out <- as.data.frame(do.call(rbind, list_data)) class(out) <- c("tbl_df", "tbl", "data.frame") out })(transect_id = transect_id)`: object 'assessments_get' not found Backtrace: ▆ 1. ├─base::suppressMessages(download_transect(4492)) at test-transect_glance.R:16:3 2. │ └─base::withCallingHandlers(...) 3. └─fqar::download_transect(4492) 4. ├─fqar:::download_transect_internal(transect_id) 5. │ ├─base::withVisible(eval(mc, parent.frame())) 6. │ └─base::eval(mc, parent.frame()) 7. │ └─base::eval(mc, parent.frame()) 8. └─fqar (local) `<fn>`(transect_id = transect_id) 9. ├─base::message(...) 10. ├─base::paste(...) 11. └─httr::status_code(assessments_get) ── Error ('test-transect_inventory.R:16:3'): transect_inventory works ────────── Error in `(function (transect_id) { if (!is.numeric(transect_id)) { stop("transect_id must be an integer.", call. = FALSE) } if (transect_id%%1 != 0) { stop("transect_id must be an integer.", call. = FALSE) } empty <- data.frame(V1 = character(0), V2 = character(0), V3 = character(0), V4 = character(0), V5 = character(0), V6 = character(0), V7 = character(0), V8 = character(0), V9 = character(0), V10 = character(0), V11 = character(0), V12 = character(0), V13 = character(0), V14 = character(0)) class(empty) <- c("tbl_df", "tbl", "data.frame") if (transect_id == -40000) { return(invisible(empty)) } trans_address <- paste0("http://universalfqa.org/get/transect/", transect_id) ua <- httr::user_agent("https://github.com/equitable-equations/fqar") trans_get <- tryCatch(httr::GET(trans_address, ua, timeout(2)), error = function(e) { message("No response from universalFQA.org. Please check internet connection.") character(0) }) cl <- class(trans_get) if (cl != "response") { return(invisible(empty)) } if (httr::http_error(trans_get)) { message(paste("API request to universalFQA.org failed. Error", httr::status_code(assessments_get))) return(invisible(empty)) } trans_text <- httr::content(trans_get, "text", encoding = "ISO-8859-1") trans_json <- jsonlite::fromJSON(trans_text) list_data <- trans_json[[2]] if ((list_data[[1]] == "The requested assessment is not public") & (!is.na(list_data[[1]]))) { message("The requested assessment is not public.") return(invisible(empty)) } max_length <- max(unlist(lapply(list_data, length))) list_data <- lapply(list_data, function(x) { length(x) <- max_length unlist(x) }) out <- as.data.frame(do.call(rbind, list_data)) class(out) <- c("tbl_df", "tbl", "data.frame") out })(transect_id = transect_id)`: object 'assessments_get' not found Backtrace: ▆ 1. ├─base::suppressMessages(download_transect(4492)) at test-transect_inventory.R:16:3 2. │ └─base::withCallingHandlers(...) 3. └─fqar::download_transect(4492) 4. ├─fqar:::download_transect_internal(transect_id) 5. │ ├─base::withVisible(eval(mc, parent.frame())) 6. │ └─base::eval(mc, parent.frame()) 7. │ └─base::eval(mc, parent.frame()) 8. └─fqar (local) `<fn>`(transect_id = transect_id) 9. ├─base::message(...) 10. ├─base::paste(...) 11. └─httr::status_code(assessments_get) ── Error ('test-transect_list_glance.R:14:3'): transect_list_glance works ────── Error in `(function (database_id) { if (!is.numeric(database_id)) { stop("database_id must be an integer corresponding to an existing FQA database. Use index_fqa_databases() to obtain a data frame of valid options.", call. = FALSE) } if (database_id%%1 != 0) { stop("database_id must be an integer corresponding to an existing FQA database. Use index_fqa_databases() to obtain a data frame of valid options.", call. = FALSE) } empty_df <- data.frame(id = numeric(0), assessment = character(0), date = numeric(0), site = character(0), practitioner = character(0)) class(empty_df) <- c("tbl_df", "tbl", "data.frame") empty_df$date <- as.Date(empty_df$date) if (database_id == -40000) { return(invisible(empty_df)) } trans_address <- paste0("http://universalfqa.org/get/database/", database_id, "/transect") ua <- httr::user_agent("https://github.com/equitable-equations/fqar") trans_get <- tryCatch(httr::GET(trans_address, ua, timeout(2)), error = function(e) { message("No response from universalFQA.org. Please check internet connection.") character(0) }) cl <- class(trans_get) if (cl != "response") { return(invisible(empty_df)) } if (httr::http_error(trans_get)) { message(paste("API request to universalFQA.org failed. Error", httr::status_code(assessments_get))) return(invisible(empty_df)) } trans_text <- httr::content(trans_get, "text", encoding = "ISO-8859-1") trans_json <- jsonlite::fromJSON(trans_text) list_data <- trans_json[[2]] transect_summary <- as.data.frame(list_data) if (nrow(transect_summary) == 0) { message("No data associated with specified database_id.") return(invisible(empty_df)) } colnames(transect_summary) <- c("id", "assessment", "date", "site", "practitioner") transect_summary$id <- as.double(transect_summary$id) transect_summary$date[transect_summary$date == "0000-00-00"] <- NA transect_summary$date <- as.Date(transect_summary$date) class(transect_summary) <- c("tbl_df", "tbl", "data.frame") transect_summary })(database_id = database_id)`: object 'assessments_get' not found Backtrace: ▆ 1. ├─base::suppressMessages(download_transect_list(63, id %in% test_vec)) at test-transect_list_glance.R:14:3 2. │ └─base::withCallingHandlers(...) 3. └─fqar::download_transect_list(63, id %in% test_vec) 4. └─fqar::index_fqa_transects(database_id) 5. ├─fqar:::index_fqa_transects_internal(database_id) 6. │ ├─base::withVisible(eval(mc, parent.frame())) 7. │ └─base::eval(mc, parent.frame()) 8. │ └─base::eval(mc, parent.frame()) 9. └─fqar (local) `<fn>`(database_id = database_id) 10. ├─base::message(...) 11. ├─base::paste(...) 12. └─httr::status_code(assessments_get) ── Error ('test-transect_list_inventory.R:9:3'): transect_list_inventory works ── Error in `(function (transect_id) { if (!is.numeric(transect_id)) { stop("transect_id must be an integer.", call. = FALSE) } if (transect_id%%1 != 0) { stop("transect_id must be an integer.", call. = FALSE) } empty <- data.frame(V1 = character(0), V2 = character(0), V3 = character(0), V4 = character(0), V5 = character(0), V6 = character(0), V7 = character(0), V8 = character(0), V9 = character(0), V10 = character(0), V11 = character(0), V12 = character(0), V13 = character(0), V14 = character(0)) class(empty) <- c("tbl_df", "tbl", "data.frame") if (transect_id == -40000) { return(invisible(empty)) } trans_address <- paste0("http://universalfqa.org/get/transect/", transect_id) ua <- httr::user_agent("https://github.com/equitable-equations/fqar") trans_get <- tryCatch(httr::GET(trans_address, ua, timeout(2)), error = function(e) { message("No response from universalFQA.org. Please check internet connection.") character(0) }) cl <- class(trans_get) if (cl != "response") { return(invisible(empty)) } if (httr::http_error(trans_get)) { message(paste("API request to universalFQA.org failed. Error", httr::status_code(assessments_get))) return(invisible(empty)) } trans_text <- httr::content(trans_get, "text", encoding = "ISO-8859-1") trans_json <- jsonlite::fromJSON(trans_text) list_data <- trans_json[[2]] if ((list_data[[1]] == "The requested assessment is not public") & (!is.na(list_data[[1]]))) { message("The requested assessment is not public.") return(invisible(empty)) } max_length <- max(unlist(lapply(list_data, length))) list_data <- lapply(list_data, function(x) { length(x) <- max_length unlist(x) }) out <- as.data.frame(do.call(rbind, list_data)) class(out) <- c("tbl_df", "tbl", "data.frame") out })(transect_id = transect_id)`: object 'assessments_get' not found Backtrace: ▆ 1. ├─base::suppressMessages(download_transect(4492)) at test-transect_list_inventory.R:9:3 2. │ └─base::withCallingHandlers(...) 3. └─fqar::download_transect(4492) 4. ├─fqar:::download_transect_internal(transect_id) 5. │ ├─base::withVisible(eval(mc, parent.frame())) 6. │ └─base::eval(mc, parent.frame()) 7. │ └─base::eval(mc, parent.frame()) 8. └─fqar (local) `<fn>`(transect_id = transect_id) 9. ├─base::message(...) 10. ├─base::paste(...) 11. └─httr::status_code(assessments_get) ── Error ('test-transect_phys.R:11:3'): transect_phys works ──────────────────── Error in `(function (transect_id) { if (!is.numeric(transect_id)) { stop("transect_id must be an integer.", call. = FALSE) } if (transect_id%%1 != 0) { stop("transect_id must be an integer.", call. = FALSE) } empty <- data.frame(V1 = character(0), V2 = character(0), V3 = character(0), V4 = character(0), V5 = character(0), V6 = character(0), V7 = character(0), V8 = character(0), V9 = character(0), V10 = character(0), V11 = character(0), V12 = character(0), V13 = character(0), V14 = character(0)) class(empty) <- c("tbl_df", "tbl", "data.frame") if (transect_id == -40000) { return(invisible(empty)) } trans_address <- paste0("http://universalfqa.org/get/transect/", transect_id) ua <- httr::user_agent("https://github.com/equitable-equations/fqar") trans_get <- tryCatch(httr::GET(trans_address, ua, timeout(2)), error = function(e) { message("No response from universalFQA.org. Please check internet connection.") character(0) }) cl <- class(trans_get) if (cl != "response") { return(invisible(empty)) } if (httr::http_error(trans_get)) { message(paste("API request to universalFQA.org failed. Error", httr::status_code(assessments_get))) return(invisible(empty)) } trans_text <- httr::content(trans_get, "text", encoding = "ISO-8859-1") trans_json <- jsonlite::fromJSON(trans_text) list_data <- trans_json[[2]] if ((list_data[[1]] == "The requested assessment is not public") & (!is.na(list_data[[1]]))) { message("The requested assessment is not public.") return(invisible(empty)) } max_length <- max(unlist(lapply(list_data, length))) list_data <- lapply(list_data, function(x) { length(x) <- max_length unlist(x) }) out <- as.data.frame(do.call(rbind, list_data)) class(out) <- c("tbl_df", "tbl", "data.frame") out })(transect_id = transect_id)`: object 'assessments_get' not found Backtrace: ▆ 1. ├─base::suppressMessages(download_transect(4492)) at test-transect_phys.R:11:3 2. │ └─base::withCallingHandlers(...) 3. └─fqar::download_transect(4492) 4. ├─fqar:::download_transect_internal(transect_id) 5. │ ├─base::withVisible(eval(mc, parent.frame())) 6. │ └─base::eval(mc, parent.frame()) 7. │ └─base::eval(mc, parent.frame()) 8. └─fqar (local) `<fn>`(transect_id = transect_id) 9. ├─base::message(...) 10. ├─base::paste(...) 11. └─httr::status_code(assessments_get) ── Error ('test-transect_subplot_inventories.R:6:3'): transect_subplot_inventories works ── Error in `(function (transect_id) { if (!is.numeric(transect_id)) { stop("transect_id must be an integer.", call. = FALSE) } if (transect_id%%1 != 0) { stop("transect_id must be an integer.", call. = FALSE) } empty <- data.frame(V1 = character(0), V2 = character(0), V3 = character(0), V4 = character(0), V5 = character(0), V6 = character(0), V7 = character(0), V8 = character(0), V9 = character(0), V10 = character(0), V11 = character(0), V12 = character(0), V13 = character(0), V14 = character(0)) class(empty) <- c("tbl_df", "tbl", "data.frame") if (transect_id == -40000) { return(invisible(empty)) } trans_address <- paste0("http://universalfqa.org/get/transect/", transect_id) ua <- httr::user_agent("https://github.com/equitable-equations/fqar") trans_get <- tryCatch(httr::GET(trans_address, ua, timeout(2)), error = function(e) { message("No response from universalFQA.org. Please check internet connection.") character(0) }) cl <- class(trans_get) if (cl != "response") { return(invisible(empty)) } if (httr::http_error(trans_get)) { message(paste("API request to universalFQA.org failed. Error", httr::status_code(assessments_get))) return(invisible(empty)) } trans_text <- httr::content(trans_get, "text", encoding = "ISO-8859-1") trans_json <- jsonlite::fromJSON(trans_text) list_data <- trans_json[[2]] if ((list_data[[1]] == "The requested assessment is not public") & (!is.na(list_data[[1]]))) { message("The requested assessment is not public.") return(invisible(empty)) } max_length <- max(unlist(lapply(list_data, length))) list_data <- lapply(list_data, function(x) { length(x) <- max_length unlist(x) }) out <- as.data.frame(do.call(rbind, list_data)) class(out) <- c("tbl_df", "tbl", "data.frame") out })(transect_id = transect_id)`: object 'assessments_get' not found Backtrace: ▆ 1. ├─base::suppressMessages(download_transect(5932)) at test-transect_subplot_inventories.R:6:3 2. │ └─base::withCallingHandlers(...) 3. └─fqar::download_transect(5932) 4. ├─fqar:::download_transect_internal(transect_id) 5. │ ├─base::withVisible(eval(mc, parent.frame())) 6. │ └─base::eval(mc, parent.frame()) 7. │ └─base::eval(mc, parent.frame()) 8. └─fqar (local) `<fn>`(transect_id = transect_id) 9. ├─base::message(...) 10. ├─base::paste(...) 11. └─httr::status_code(assessments_get) [ FAIL 24 | WARN 0 | SKIP 0 | PASS 231 ] Error: Test failures Execution halted Flavor: r-devel-windows-x86_64

Version: 0.5.3
Check: tests
Result: ERROR Running ‘testthat.R’ [10s/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/tests.html > # * https://testthat.r-lib.org/reference/test_package.html#special-files > > library(testthat) > library(fqar) > > test_check("fqar") data_set must be a dataframe obtained from the universalFQA.org website. Type ?download_transect for help. data_set must be a dataframe obtained from the universalFQA.org website. Type ?download_transect for help. [ FAIL 2 | WARN 0 | SKIP 0 | PASS 363 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-download_database.R:10:3'): download_database works ──────────── Error in `(function (database_id) { if (!is.numeric(database_id)) { stop("database_id must be an integer.", call. = FALSE) } if (database_id%%1 != 0) { stop("database_id must be an integer.", call. = FALSE) } empty <- data.frame(V1 = character(0), V2 = character(0), V3 = character(0), V4 = character(0), V5 = character(0), V6 = character(0), V7 = character(0), V8 = character(0), V9 = character(0)) class(empty) <- c("tbl_df", "tbl", "data.frame") if (database_id == -40000) { return(invisible(empty)) } database_address <- paste0("http://universalfqa.org/get/database/", database_id) ua <- httr::user_agent("https://github.com/equitable-equations/fqar") database_get <- tryCatch(httr::GET(database_address, ua, timeout(2)), error = function(e) { message("No response from universalFQA.org. Please check internet connection.") character(0) }) cl <- class(database_get) if (cl != "response") { return(invisible(empty)) } if (httr::http_error(database_get)) { message(paste("API request to universalFQA.org failed. Error", httr::status_code(assessments_get))) return(invisible(empty)) } database_text <- httr::content(database_get, "text", encoding = "ISO-8859-1") database_json <- jsonlite::fromJSON(database_text) list_data <- database_json[[2]] if ((list_data[[1]] == "The requested assessment is not public") & (!is.na(list_data[[1]]))) { message("The requested assessment is not public.") return(invisible(empty)) } max_length <- max(unlist(lapply(list_data, length))) list_data <- lapply(list_data, function(x) { length(x) <- max_length unlist(x) }) db_out <- as.data.frame(do.call(rbind, list_data)) if (db_out[5, 2] == 0) { message("Specified database is empty.") } class(db_out) <- c("tbl_df", "tbl", "data.frame") db_out })(database_id = database_id)`: object 'assessments_get' not found Backtrace: ▆ 1. ├─testthat::expect_message(download_database(3)) at test-download_database.R:10:3 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. └─fqar::download_database(3) 8. ├─fqar:::download_database_internal(database_id) 9. │ ├─base::withVisible(eval(mc, parent.frame())) 10. │ └─base::eval(mc, parent.frame()) 11. │ └─base::eval(mc, parent.frame()) 12. └─fqar (local) `<fn>`(database_id = database_id) 13. ├─base::message(...) 14. ├─base::paste(...) 15. └─httr::status_code(assessments_get) ── Error ('test-species_acronym.R:14:3'): species_acronym works ──────────────── Error: parse error: unallowed token at this point in JSON text tatus" : "success", "data" : } (right here) ------^ Backtrace: ▆ 1. ├─base::suppressMessages(download_database(149)) at test-species_acronym.R:14:3 2. │ └─base::withCallingHandlers(...) 3. └─fqar::download_database(149) 4. ├─fqar:::download_database_internal(database_id) 5. │ ├─base::withVisible(eval(mc, parent.frame())) 6. │ └─base::eval(mc, parent.frame()) 7. │ └─base::eval(mc, parent.frame()) 8. └─fqar (local) `<fn>`(database_id = database_id) 9. └─jsonlite::fromJSON(database_text) 10. └─jsonlite:::parse_and_simplify(...) 11. └─jsonlite:::parseJSON(txt, bigint_as_char) 12. └─jsonlite:::parse_string(txt, bigint_as_char) [ FAIL 2 | WARN 0 | SKIP 0 | PASS 363 ] Error: Test failures Execution halted Flavor: r-release-linux-x86_64

Version: 0.5.3
Check: examples
Result: ERROR Running examples in 'fqar-Ex.R' failed The error most likely occurred in: > ### Name: species_acronym > ### Title: Acronym of a species in a specified database > ### Aliases: species_acronym > > ### ** Examples > > species_acronym("Anemone canadensis", database_id = 149) Error: parse error: unallowed token at this point in JSON text tatus" : "success", "data" : } (right here) ------^ Execution halted Flavors: r-release-windows-x86_64, r-oldrel-windows-x86_64

Version: 0.5.3
Check: tests
Result: ERROR Running 'testthat.R' [28s] 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/tests.html > # * https://testthat.r-lib.org/reference/test_package.html#special-files > > library(testthat) > library(fqar) > > test_check("fqar") data_set must be a dataframe obtained from the universalFQA.org website. Type ?download_transect for help. data_set must be a dataframe obtained from the universalFQA.org website. Type ?download_transect for help. [ FAIL 2 | WARN 0 | SKIP 0 | PASS 358 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-download_database.R:10:3'): download_database works ──────────── Error in `(function (database_id) { if (!is.numeric(database_id)) { stop("database_id must be an integer.", call. = FALSE) } if (database_id%%1 != 0) { stop("database_id must be an integer.", call. = FALSE) } empty <- data.frame(V1 = character(0), V2 = character(0), V3 = character(0), V4 = character(0), V5 = character(0), V6 = character(0), V7 = character(0), V8 = character(0), V9 = character(0)) class(empty) <- c("tbl_df", "tbl", "data.frame") if (database_id == -40000) { return(invisible(empty)) } database_address <- paste0("http://universalfqa.org/get/database/", database_id) ua <- httr::user_agent("https://github.com/equitable-equations/fqar") database_get <- tryCatch(httr::GET(database_address, ua, timeout(2)), error = function(e) { message("No response from universalFQA.org. Please check internet connection.") character(0) }) cl <- class(database_get) if (cl != "response") { return(invisible(empty)) } if (httr::http_error(database_get)) { message(paste("API request to universalFQA.org failed. Error", httr::status_code(assessments_get))) return(invisible(empty)) } database_text <- httr::content(database_get, "text", encoding = "ISO-8859-1") database_json <- jsonlite::fromJSON(database_text) list_data <- database_json[[2]] if ((list_data[[1]] == "The requested assessment is not public") & (!is.na(list_data[[1]]))) { message("The requested assessment is not public.") return(invisible(empty)) } max_length <- max(unlist(lapply(list_data, length))) list_data <- lapply(list_data, function(x) { length(x) <- max_length unlist(x) }) db_out <- as.data.frame(do.call(rbind, list_data)) if (db_out[5, 2] == 0) { message("Specified database is empty.") } class(db_out) <- c("tbl_df", "tbl", "data.frame") db_out })(database_id = database_id)`: object 'assessments_get' not found Backtrace: ▆ 1. ├─testthat::expect_message(download_database(3)) at test-download_database.R:10:3 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. └─fqar::download_database(3) 8. ├─fqar:::download_database_internal(database_id) 9. │ ├─base::withVisible(eval(mc, parent.frame())) 10. │ └─base::eval(mc, parent.frame()) 11. │ └─base::eval(mc, parent.frame()) 12. └─fqar (local) `<fn>`(database_id = database_id) 13. ├─base::message(...) 14. ├─base::paste(...) 15. └─httr::status_code(assessments_get) ── Error ('test-species_acronym.R:14:3'): species_acronym works ──────────────── Error: parse error: unallowed token at this point in JSON text tatus" : "success", "data" : } (right here) ------^ Backtrace: ▆ 1. ├─base::suppressMessages(download_database(149)) at test-species_acronym.R:14:3 2. │ └─base::withCallingHandlers(...) 3. └─fqar::download_database(149) 4. ├─fqar:::download_database_internal(database_id) 5. │ ├─base::withVisible(eval(mc, parent.frame())) 6. │ └─base::eval(mc, parent.frame()) 7. │ └─base::eval(mc, parent.frame()) 8. └─fqar (local) `<fn>`(database_id = database_id) 9. └─jsonlite::fromJSON(database_text) 10. └─jsonlite:::parse_and_simplify(...) 11. └─jsonlite:::parseJSON(txt, bigint_as_char) 12. └─jsonlite:::parse_string(txt, bigint_as_char) [ FAIL 2 | WARN 0 | SKIP 0 | PASS 358 ] Error: Test failures Execution halted Flavor: r-release-windows-x86_64

Version: 0.5.3
Check: tests
Result: ERROR Running 'testthat.R' [31s] 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/tests.html > # * https://testthat.r-lib.org/reference/test_package.html#special-files > > library(testthat) > library(fqar) > > test_check("fqar") data_set must be a dataframe obtained from the universalFQA.org website. Type ?download_transect for help. data_set must be a dataframe obtained from the universalFQA.org website. Type ?download_transect for help. [ FAIL 2 | WARN 0 | SKIP 0 | PASS 363 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-download_database.R:10:3'): download_database works ──────────── Error in `(function (database_id) { if (!is.numeric(database_id)) { stop("database_id must be an integer.", call. = FALSE) } if (database_id%%1 != 0) { stop("database_id must be an integer.", call. = FALSE) } empty <- data.frame(V1 = character(0), V2 = character(0), V3 = character(0), V4 = character(0), V5 = character(0), V6 = character(0), V7 = character(0), V8 = character(0), V9 = character(0)) class(empty) <- c("tbl_df", "tbl", "data.frame") if (database_id == -40000) { return(invisible(empty)) } database_address <- paste0("http://universalfqa.org/get/database/", database_id) ua <- httr::user_agent("https://github.com/equitable-equations/fqar") database_get <- tryCatch(httr::GET(database_address, ua, timeout(2)), error = function(e) { message("No response from universalFQA.org. Please check internet connection.") character(0) }) cl <- class(database_get) if (cl != "response") { return(invisible(empty)) } if (httr::http_error(database_get)) { message(paste("API request to universalFQA.org failed. Error", httr::status_code(assessments_get))) return(invisible(empty)) } database_text <- httr::content(database_get, "text", encoding = "ISO-8859-1") database_json <- jsonlite::fromJSON(database_text) list_data <- database_json[[2]] if ((list_data[[1]] == "The requested assessment is not public") & (!is.na(list_data[[1]]))) { message("The requested assessment is not public.") return(invisible(empty)) } max_length <- max(unlist(lapply(list_data, length))) list_data <- lapply(list_data, function(x) { length(x) <- max_length unlist(x) }) db_out <- as.data.frame(do.call(rbind, list_data)) if (db_out[5, 2] == 0) { message("Specified database is empty.") } class(db_out) <- c("tbl_df", "tbl", "data.frame") db_out })(database_id = database_id)`: object 'assessments_get' not found Backtrace: ▆ 1. ├─testthat::expect_message(download_database(3)) at test-download_database.R:10:3 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. └─fqar::download_database(3) 8. ├─fqar:::download_database_internal(database_id) 9. │ ├─base::withVisible(eval(mc, parent.frame())) 10. │ └─base::eval(mc, parent.frame()) 11. │ └─base::eval(mc, parent.frame()) 12. └─fqar (local) `<fn>`(database_id = database_id) 13. ├─base::message(...) 14. ├─base::paste(...) 15. └─httr::status_code(assessments_get) ── Error ('test-species_acronym.R:14:3'): species_acronym works ──────────────── Error: parse error: unallowed token at this point in JSON text tatus" : "success", "data" : } (right here) ------^ Backtrace: ▆ 1. ├─base::suppressMessages(download_database(149)) at test-species_acronym.R:14:3 2. │ └─base::withCallingHandlers(...) 3. └─fqar::download_database(149) 4. ├─fqar:::download_database_internal(database_id) 5. │ ├─base::withVisible(eval(mc, parent.frame())) 6. │ └─base::eval(mc, parent.frame()) 7. │ └─base::eval(mc, parent.frame()) 8. └─fqar (local) `<fn>`(database_id = database_id) 9. └─jsonlite::fromJSON(database_text) 10. └─jsonlite:::parse_and_simplify(...) 11. └─jsonlite:::parseJSON(txt, bigint_as_char) 12. └─jsonlite:::parse_string(txt, bigint_as_char) [ FAIL 2 | WARN 0 | SKIP 0 | PASS 363 ] Error: Test failures Execution halted Flavor: r-oldrel-windows-x86_64