Last updated on 2025-07-21 12:50:13 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.3.0 | 2.77 | 43.99 | 46.76 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.3.0 | 1.88 | 32.78 | 34.66 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.3.0 | 63.61 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 1.3.0 | 74.39 | ERROR | |||
| r-devel-windows-x86_64 | 1.3.0 | 4.00 | 102.00 | 106.00 | OK | |
| r-patched-linux-x86_64 | 1.3.0 | 2.93 | 40.25 | 43.18 | OK | |
| r-release-linux-x86_64 | 1.3.0 | 2.81 | 40.14 | 42.95 | OK | |
| r-release-macos-arm64 | 1.3.0 | 79.00 | OK | |||
| r-release-macos-x86_64 | 1.3.0 | 94.00 | OK | |||
| r-release-windows-x86_64 | 1.3.0 | 5.00 | 103.00 | 108.00 | OK | |
| r-oldrel-macos-arm64 | 1.3.0 | 68.00 | OK | |||
| r-oldrel-macos-x86_64 | 1.3.0 | 82.00 | OK | |||
| r-oldrel-windows-x86_64 | 1.3.0 | 6.00 | 113.00 | 119.00 | OK |
Version: 1.3.0
Check: tests
Result: ERROR
Running ‘test-all.R’ [11s/40s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
> library(testthat)
> library(rcites)
> library(tibble)
> test_check("rcites")
v Token stored for the session.
[ FAIL 28 | WARN 15 | SKIP 5 | PASS 42 ]
══ Skipped tests (5) ═══════════════════════════════════════════════════════════
• On CRAN (5): 'test-distributions.R:13:5', 'test-distributions.R:20:5',
'test-legislations.R:16:5', 'test-references.R:11:3', 'test-token.R:9:5'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-distributions.R:11:5'): spp_distributions() defaults work ────
all(unlist(lapply(res, function(x) is_cl_df(x)))) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-distributions.R:12:5'): spp_distributions() defaults work ────
lang_GQ %in% res$distributions$name (`actual`) not identical to c(TRUE, FALSE, FALSE) (`expected`).
`actual`: FALSE FALSE FALSE
`expected`: TRUE FALSE FALSE
── Failure ('test-distributions.R:18:7'): spp_distributions() works when no info available ──
`res <- spp_distributions(taxon_id = 0)` did not throw the expected warning.
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-distributions.R:17:5
2. │ └─cassette$call_block(...)
3. └─testthat::expect_warning(res <- spp_distributions(taxon_id = 0)) at test-distributions.R:18:7
── Error ('test-distributions.R:25:7'): spp_distributions() raw mode works ─────
Error in `class(out) <- c("list", "spp_raw")`: attempt to set an attribute on NULL
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-distributions.R:24:5
2. │ └─cassette$call_block(...)
3. ├─testthat::expect_silent(...) at test-distributions.R:25:7
4. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
5. │ ├─testthat (local) .capture(...)
6. │ │ ├─withr::with_output_sink(...)
7. │ │ │ └─base::force(code)
8. │ │ ├─base::withCallingHandlers(...)
9. │ │ └─base::withVisible(code)
10. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
11. └─rcites::spp_distributions(taxon_id = tx_id, raw = TRUE, verbose = FALSE)
── Failure ('test-distributions.R:44:5'): spp_distributions() language works ───
lang_GQ %in% res1$distributions$name (`actual`) not identical to c(FALSE, TRUE, FALSE) (`expected`).
`actual`: FALSE FALSE FALSE
`expected`: FALSE TRUE FALSE
── Error ('test-distributions.R:50:7'): spp_distributions() batch mode works ───
Error in `class(out) <- c("list", "spp_raw")`: attempt to set an attribute on NULL
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-distributions.R:48:5
2. │ └─cassette$call_block(...)
3. └─rcites::spp_distributions(...) at test-distributions.R:50:7
4. └─base::lapply(...)
5. └─rcites (local) FUN(X[[i]], ...)
── Failure ('test-distributions.R:67:5'): spp_distributions() edge case: one distribution ──
dim(res$distribution)[1] (`actual`) not equal to 1 (`expected`).
`actual`: 0.0
`expected`: 1.0
── Failure ('test-legislations.R:13:5'): spp_cites_legislation() defaults work ──
res$cites_suspensions$applies_to_import has type 'NULL', not 'logical'.
── Failure ('test-legislations.R:14:5'): spp_cites_legislation() defaults work ──
res$cites_quotas$public_display has type 'NULL', not 'logical'.
── Failure ('test-legislations.R:15:5'): spp_cites_legislation() defaults work ──
"Guinea" %in% res$cites_suspensions$geo_entity.name is not TRUE
`actual`: FALSE
`expected`: TRUE
── Error ('test-legislations.R:21:7'): spp_cites_legislation() raw mode works ──
Error in `class(out) <- c("list", "spp_raw")`: attempt to set an attribute on NULL
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-legislations.R:20:5
2. │ └─cassette$call_block(...)
3. ├─testthat::expect_silent(...) at test-legislations.R:21:7
4. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
5. │ ├─testthat (local) .capture(...)
6. │ │ ├─withr::with_output_sink(...)
7. │ │ │ └─base::force(code)
8. │ │ ├─base::withCallingHandlers(...)
9. │ │ └─base::withVisible(code)
10. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
11. └─rcites::spp_cites_legislation(taxon_id = tx_id, raw = TRUE, verbose = FALSE)
── Failure ('test-legislations.R:46:5'): spp_cites_legislation() scope & language works ──
!all(res$cites_listings$is_current) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-legislations.R:47:5'): spp_cites_legislation() scope & language works ──
"Guinée" %in% res$cites_suspensions$geo_entity.name is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-legislations.R:54:5'): spp_eu_legislation() defaults works ───
nrow(res$eu_listings) (`actual`) not equal to 2 (`expected`).
`actual`: 0.0
`expected`: 2.0
── Failure ('test-legislations.R:55:5'): spp_eu_legislation() defaults works ───
"Namibia" %in% res$eu_decisions$geo_entity.name is not TRUE
`actual`: FALSE
`expected`: TRUE
── Error ('test-legislations.R:64:7'): spp_eu_legislation() raw mode works ─────
Error in `class(out) <- c("list", "spp_raw")`: attempt to set an attribute on NULL
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-legislations.R:63:5
2. │ └─cassette$call_block(...)
3. ├─testthat::expect_silent(...) at test-legislations.R:64:7
4. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
5. │ ├─testthat (local) .capture(...)
6. │ │ ├─withr::with_output_sink(...)
7. │ │ │ └─base::force(code)
8. │ │ ├─base::withCallingHandlers(...)
9. │ │ └─base::withVisible(code)
10. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
11. └─rcites::spp_eu_legislation(taxon_id = tx_id, raw = TRUE, verbose = FALSE)
── Failure ('test-legislations.R:89:5'): spp_cites_legislation() scope & lang works ──
!all(res$eu_listings$is_current) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-legislations.R:90:5'): spp_cites_legislation() scope & lang works ──
"Namibie" %in% res$eu_decisions$geo_entity.name is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-legislations.R:102:5'): spp_cites_legislation() batch mode works ──
unique(res$cites_listings$taxon_id) (`actual`) not identical to c(tx_id, tx_id2) (`expected`).
`actual` is NULL
`expected` is a character vector ('4521', '3210')
── Failure ('test-legislations.R:119:5'): spp_cites_legislation() batch mode works ──
unique(res$eu_listings$taxon_id) (`actual`) not identical to c(tx_id, tx_id2) (`expected`).
`actual` is NULL
`expected` is a character vector ('4521', '3210')
── Error ('test-references.R:16:5'): spp_references() raw mode ─────────────────
Error in `class(out) <- c("list", "spp_raw")`: attempt to set an attribute on NULL
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-references.R:15:3
2. │ └─cassette$call_block(...)
3. ├─testthat::expect_silent(...) at test-references.R:16:5
4. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
5. │ ├─testthat (local) .capture(...)
6. │ │ ├─withr::with_output_sink(...)
7. │ │ │ └─base::force(code)
8. │ │ ├─base::withCallingHandlers(...)
9. │ │ └─base::withVisible(code)
10. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
11. └─rcites::spp_references(taxon_id = tx_id, raw = TRUE, verbose = FALSE)
── Failure ('test-references.R:40:3'): spp_references() batch mode works ───────
unique(res$references$taxon_id) (`actual`) not identical to c(tx_id, tx_id2) (`expected`).
`actual` is NULL
`expected` is a character vector ('4521', '3210')
── Error ('test-references.R:45:5'): spp_references() raw batch mode works ─────
Error in `class(out) <- c("list", "spp_raw")`: attempt to set an attribute on NULL
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-references.R:44:3
2. │ └─cassette$call_block(...)
3. └─rcites::spp_references(...) at test-references.R:45:5
4. └─base::lapply(...)
5. └─rcites (local) FUN(X[[i]], ...)
── Error ('test-taxonconcept.R:12:5'): spp_taxonconcept() defaults work ────────
Error in `if (!pag) {
warning("Taxon not listed.")
return(NULL)
} else {
if (pag > 1) {
if (is.null(pages))
pages <- seq_len(pag)
else pages <- pages[pages <= pag]
if (!length(pages))
stop("Only page 1-", pag, " are available.")
if (length(pages) > 1) {
res <- rcites_autopagination(q_url, per_page, pages[-1L],
pag, token, verbose, ...)
tmp2 <- c(tmp$taxon_concepts, do.call(c, lapply(res,
function(x) x$taxon_concepts)))
}
else tmp2 <- tmp$taxon_concepts
}
else tmp2 <- tmp$taxon_concepts
if (raw) {
class(tmp2) <- c("list", "spp_raw")
return(tmp2)
}
else {
sp_nm <- c("synonyms", "higher_taxa", "common_names",
"cites_listing", "cites_listings", "accepted_names")
out <- list()
out$all_id <- rcites_taxonconcept_allentries(tmp2, sp_nm)
out$all_id$updated_at <- as.POSIXlt(out$all_id$updated_at,
format = "%Y-%m-%dT%H:%M:%OS")
out$all_id$active <- as.logical(out$all_id$active)
id <- which(out$all_id$active)
out$general <- out$all_id[out$all_id$active, ]
out$higher_taxa <- rcites_taxonconcept_higher_taxa(tmp2[id],
out$general$id)
out$accepted_names <- rcites_taxonconcept_names(tmp2[!id],
"accepted_names", out$all_id$id[!id])
out$common_names <- rcites_taxonconcept_names(tmp2[id],
"common_names", out$general$id)
out$synonyms <- rcites_taxonconcept_names(tmp2[id], "synonyms",
out$general$id)
if (taxonomy == "CITES") {
tmp_cit <- lapply(tmp2[id], function(x) x$cites_listing)
out$general$cites_listing <- unlist(lapply(tmp_cit,
rcites_null_to_na))
out$cites_listings <- rcites_taxonconcept_cites_listings(tmp2[id],
out$general$id)
}
class(out$general) <- class(out$all_id) <- c("tbl_df",
"tbl", "data.frame")
class(out) <- c("spp_taxon")
attr(out, "taxonomy") <- taxonomy
}
}`: argument is of length zero
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-taxonconcept.R:11:3
2. │ └─cassette$call_block(...)
3. ├─base::suppressMessages(res <- spp_taxonconcept(query_taxon = tx_nm)) at test-taxonconcept.R:12:5
4. │ └─base::withCallingHandlers(...)
5. └─rcites::spp_taxonconcept(query_taxon = tx_nm)
── Error ('test-taxonconcept.R:29:7'): spp_taxonconcept() raw mode works ───────
Error in `if (!pag) {
warning("Taxon not listed.")
return(NULL)
} else {
if (pag > 1) {
if (is.null(pages))
pages <- seq_len(pag)
else pages <- pages[pages <= pag]
if (!length(pages))
stop("Only page 1-", pag, " are available.")
if (length(pages) > 1) {
res <- rcites_autopagination(q_url, per_page, pages[-1L],
pag, token, verbose, ...)
tmp2 <- c(tmp$taxon_concepts, do.call(c, lapply(res,
function(x) x$taxon_concepts)))
}
else tmp2 <- tmp$taxon_concepts
}
else tmp2 <- tmp$taxon_concepts
if (raw) {
class(tmp2) <- c("list", "spp_raw")
return(tmp2)
}
else {
sp_nm <- c("synonyms", "higher_taxa", "common_names",
"cites_listing", "cites_listings", "accepted_names")
out <- list()
out$all_id <- rcites_taxonconcept_allentries(tmp2, sp_nm)
out$all_id$updated_at <- as.POSIXlt(out$all_id$updated_at,
format = "%Y-%m-%dT%H:%M:%OS")
out$all_id$active <- as.logical(out$all_id$active)
id <- which(out$all_id$active)
out$general <- out$all_id[out$all_id$active, ]
out$higher_taxa <- rcites_taxonconcept_higher_taxa(tmp2[id],
out$general$id)
out$accepted_names <- rcites_taxonconcept_names(tmp2[!id],
"accepted_names", out$all_id$id[!id])
out$common_names <- rcites_taxonconcept_names(tmp2[id],
"common_names", out$general$id)
out$synonyms <- rcites_taxonconcept_names(tmp2[id], "synonyms",
out$general$id)
if (taxonomy == "CITES") {
tmp_cit <- lapply(tmp2[id], function(x) x$cites_listing)
out$general$cites_listing <- unlist(lapply(tmp_cit,
rcites_null_to_na))
out$cites_listings <- rcites_taxonconcept_cites_listings(tmp2[id],
out$general$id)
}
class(out$general) <- class(out$all_id) <- c("tbl_df",
"tbl", "data.frame")
class(out) <- c("spp_taxon")
attr(out, "taxonomy") <- taxonomy
}
}`: argument is of length zero
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-taxonconcept.R:28:5
2. │ └─cassette$call_block(...)
3. ├─testthat::expect_silent(...) at test-taxonconcept.R:29:7
4. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
5. │ ├─testthat (local) .capture(...)
6. │ │ ├─withr::with_output_sink(...)
7. │ │ │ └─base::force(code)
8. │ │ ├─base::withCallingHandlers(...)
9. │ │ └─base::withVisible(code)
10. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
11. └─rcites::spp_taxonconcept(query_taxon = tx_nm, raw = TRUE, verbose = FALSE)
── Error ('test-taxonconcept.R:43:7'): spp_taxonconcept() CMS works ────────────
Error in `if (!pag) {
warning("Taxon not listed.")
return(NULL)
} else {
if (pag > 1) {
if (is.null(pages))
pages <- seq_len(pag)
else pages <- pages[pages <= pag]
if (!length(pages))
stop("Only page 1-", pag, " are available.")
if (length(pages) > 1) {
res <- rcites_autopagination(q_url, per_page, pages[-1L],
pag, token, verbose, ...)
tmp2 <- c(tmp$taxon_concepts, do.call(c, lapply(res,
function(x) x$taxon_concepts)))
}
else tmp2 <- tmp$taxon_concepts
}
else tmp2 <- tmp$taxon_concepts
if (raw) {
class(tmp2) <- c("list", "spp_raw")
return(tmp2)
}
else {
sp_nm <- c("synonyms", "higher_taxa", "common_names",
"cites_listing", "cites_listings", "accepted_names")
out <- list()
out$all_id <- rcites_taxonconcept_allentries(tmp2, sp_nm)
out$all_id$updated_at <- as.POSIXlt(out$all_id$updated_at,
format = "%Y-%m-%dT%H:%M:%OS")
out$all_id$active <- as.logical(out$all_id$active)
id <- which(out$all_id$active)
out$general <- out$all_id[out$all_id$active, ]
out$higher_taxa <- rcites_taxonconcept_higher_taxa(tmp2[id],
out$general$id)
out$accepted_names <- rcites_taxonconcept_names(tmp2[!id],
"accepted_names", out$all_id$id[!id])
out$common_names <- rcites_taxonconcept_names(tmp2[id],
"common_names", out$general$id)
out$synonyms <- rcites_taxonconcept_names(tmp2[id], "synonyms",
out$general$id)
if (taxonomy == "CITES") {
tmp_cit <- lapply(tmp2[id], function(x) x$cites_listing)
out$general$cites_listing <- unlist(lapply(tmp_cit,
rcites_null_to_na))
out$cites_listings <- rcites_taxonconcept_cites_listings(tmp2[id],
out$general$id)
}
class(out$general) <- class(out$all_id) <- c("tbl_df",
"tbl", "data.frame")
class(out) <- c("spp_taxon")
attr(out, "taxonomy") <- taxonomy
}
}`: argument is of length zero
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-taxonconcept.R:42:5
2. │ └─cassette$call_block(...)
3. └─rcites::spp_taxonconcept(...) at test-taxonconcept.R:43:7
── Error ('test-taxonconcept.R:54:7'): spp_taxonconcept() page selection works ──
Error in `if (!pag) {
warning("Taxon not listed.")
return(NULL)
} else {
if (pag > 1) {
if (is.null(pages))
pages <- seq_len(pag)
else pages <- pages[pages <= pag]
if (!length(pages))
stop("Only page 1-", pag, " are available.")
if (length(pages) > 1) {
res <- rcites_autopagination(q_url, per_page, pages[-1L],
pag, token, verbose, ...)
tmp2 <- c(tmp$taxon_concepts, do.call(c, lapply(res,
function(x) x$taxon_concepts)))
}
else tmp2 <- tmp$taxon_concepts
}
else tmp2 <- tmp$taxon_concepts
if (raw) {
class(tmp2) <- c("list", "spp_raw")
return(tmp2)
}
else {
sp_nm <- c("synonyms", "higher_taxa", "common_names",
"cites_listing", "cites_listings", "accepted_names")
out <- list()
out$all_id <- rcites_taxonconcept_allentries(tmp2, sp_nm)
out$all_id$updated_at <- as.POSIXlt(out$all_id$updated_at,
format = "%Y-%m-%dT%H:%M:%OS")
out$all_id$active <- as.logical(out$all_id$active)
id <- which(out$all_id$active)
out$general <- out$all_id[out$all_id$active, ]
out$higher_taxa <- rcites_taxonconcept_higher_taxa(tmp2[id],
out$general$id)
out$accepted_names <- rcites_taxonconcept_names(tmp2[!id],
"accepted_names", out$all_id$id[!id])
out$common_names <- rcites_taxonconcept_names(tmp2[id],
"common_names", out$general$id)
out$synonyms <- rcites_taxonconcept_names(tmp2[id], "synonyms",
out$general$id)
if (taxonomy == "CITES") {
tmp_cit <- lapply(tmp2[id], function(x) x$cites_listing)
out$general$cites_listing <- unlist(lapply(tmp_cit,
rcites_null_to_na))
out$cites_listings <- rcites_taxonconcept_cites_listings(tmp2[id],
out$general$id)
}
class(out$general) <- class(out$all_id) <- c("tbl_df",
"tbl", "data.frame")
class(out) <- c("spp_taxon")
attr(out, "taxonomy") <- taxonomy
}
}`: argument is of length zero
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-taxonconcept.R:53:5
2. │ └─cassette$call_block(...)
3. └─rcites::spp_taxonconcept(...) at test-taxonconcept.R:54:7
── Error ('test-taxonconcept.R:66:5'): spp_taxonconcept() updated_since works ──
Error in `if (!pag) {
warning("Taxon not listed.")
return(NULL)
} else {
if (pag > 1) {
if (is.null(pages))
pages <- seq_len(pag)
else pages <- pages[pages <= pag]
if (!length(pages))
stop("Only page 1-", pag, " are available.")
if (length(pages) > 1) {
res <- rcites_autopagination(q_url, per_page, pages[-1L],
pag, token, verbose, ...)
tmp2 <- c(tmp$taxon_concepts, do.call(c, lapply(res,
function(x) x$taxon_concepts)))
}
else tmp2 <- tmp$taxon_concepts
}
else tmp2 <- tmp$taxon_concepts
if (raw) {
class(tmp2) <- c("list", "spp_raw")
return(tmp2)
}
else {
sp_nm <- c("synonyms", "higher_taxa", "common_names",
"cites_listing", "cites_listings", "accepted_names")
out <- list()
out$all_id <- rcites_taxonconcept_allentries(tmp2, sp_nm)
out$all_id$updated_at <- as.POSIXlt(out$all_id$updated_at,
format = "%Y-%m-%dT%H:%M:%OS")
out$all_id$active <- as.logical(out$all_id$active)
id <- which(out$all_id$active)
out$general <- out$all_id[out$all_id$active, ]
out$higher_taxa <- rcites_taxonconcept_higher_taxa(tmp2[id],
out$general$id)
out$accepted_names <- rcites_taxonconcept_names(tmp2[!id],
"accepted_names", out$all_id$id[!id])
out$common_names <- rcites_taxonconcept_names(tmp2[id],
"common_names", out$general$id)
out$synonyms <- rcites_taxonconcept_names(tmp2[id], "synonyms",
out$general$id)
if (taxonomy == "CITES") {
tmp_cit <- lapply(tmp2[id], function(x) x$cites_listing)
out$general$cites_listing <- unlist(lapply(tmp_cit,
rcites_null_to_na))
out$cites_listings <- rcites_taxonconcept_cites_listings(tmp2[id],
out$general$id)
}
class(out$general) <- class(out$all_id) <- c("tbl_df",
"tbl", "data.frame")
class(out) <- c("spp_taxon")
attr(out, "taxonomy") <- taxonomy
}
}`: argument is of length zero
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-taxonconcept.R:65:3
2. │ └─cassette$call_block(...)
3. └─rcites::spp_taxonconcept(...) at test-taxonconcept.R:66:5
[ FAIL 28 | WARN 15 | SKIP 5 | PASS 42 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.3.0
Check: tests
Result: ERROR
Running ‘test-all.R’ [11s/37s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
> library(testthat)
> library(rcites)
> library(tibble)
> test_check("rcites")
v Token stored for the session.
[ FAIL 28 | WARN 15 | SKIP 5 | PASS 42 ]
══ Skipped tests (5) ═══════════════════════════════════════════════════════════
• On CRAN (5): 'test-distributions.R:13:5', 'test-distributions.R:20:5',
'test-legislations.R:16:5', 'test-references.R:11:3', 'test-token.R:9:5'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-distributions.R:11:5'): spp_distributions() defaults work ────
all(unlist(lapply(res, function(x) is_cl_df(x)))) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-distributions.R:12:5'): spp_distributions() defaults work ────
lang_GQ %in% res$distributions$name (`actual`) not identical to c(TRUE, FALSE, FALSE) (`expected`).
`actual`: FALSE FALSE FALSE
`expected`: TRUE FALSE FALSE
── Failure ('test-distributions.R:18:7'): spp_distributions() works when no info available ──
`res <- spp_distributions(taxon_id = 0)` did not throw the expected warning.
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-distributions.R:17:5
2. │ └─cassette$call_block(...)
3. └─testthat::expect_warning(res <- spp_distributions(taxon_id = 0)) at test-distributions.R:18:7
── Error ('test-distributions.R:25:7'): spp_distributions() raw mode works ─────
Error in `class(out) <- c("list", "spp_raw")`: attempt to set an attribute on NULL
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-distributions.R:24:5
2. │ └─cassette$call_block(...)
3. ├─testthat::expect_silent(...) at test-distributions.R:25:7
4. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
5. │ ├─testthat (local) .capture(...)
6. │ │ ├─withr::with_output_sink(...)
7. │ │ │ └─base::force(code)
8. │ │ ├─base::withCallingHandlers(...)
9. │ │ └─base::withVisible(code)
10. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
11. └─rcites::spp_distributions(taxon_id = tx_id, raw = TRUE, verbose = FALSE)
── Failure ('test-distributions.R:44:5'): spp_distributions() language works ───
lang_GQ %in% res1$distributions$name (`actual`) not identical to c(FALSE, TRUE, FALSE) (`expected`).
`actual`: FALSE FALSE FALSE
`expected`: FALSE TRUE FALSE
── Error ('test-distributions.R:50:7'): spp_distributions() batch mode works ───
Error in `class(out) <- c("list", "spp_raw")`: attempt to set an attribute on NULL
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-distributions.R:48:5
2. │ └─cassette$call_block(...)
3. └─rcites::spp_distributions(...) at test-distributions.R:50:7
4. └─base::lapply(...)
5. └─rcites (local) FUN(X[[i]], ...)
── Failure ('test-distributions.R:67:5'): spp_distributions() edge case: one distribution ──
dim(res$distribution)[1] (`actual`) not equal to 1 (`expected`).
`actual`: 0.0
`expected`: 1.0
── Failure ('test-legislations.R:13:5'): spp_cites_legislation() defaults work ──
res$cites_suspensions$applies_to_import has type 'NULL', not 'logical'.
── Failure ('test-legislations.R:14:5'): spp_cites_legislation() defaults work ──
res$cites_quotas$public_display has type 'NULL', not 'logical'.
── Failure ('test-legislations.R:15:5'): spp_cites_legislation() defaults work ──
"Guinea" %in% res$cites_suspensions$geo_entity.name is not TRUE
`actual`: FALSE
`expected`: TRUE
── Error ('test-legislations.R:21:7'): spp_cites_legislation() raw mode works ──
Error in `class(out) <- c("list", "spp_raw")`: attempt to set an attribute on NULL
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-legislations.R:20:5
2. │ └─cassette$call_block(...)
3. ├─testthat::expect_silent(...) at test-legislations.R:21:7
4. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
5. │ ├─testthat (local) .capture(...)
6. │ │ ├─withr::with_output_sink(...)
7. │ │ │ └─base::force(code)
8. │ │ ├─base::withCallingHandlers(...)
9. │ │ └─base::withVisible(code)
10. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
11. └─rcites::spp_cites_legislation(taxon_id = tx_id, raw = TRUE, verbose = FALSE)
── Failure ('test-legislations.R:46:5'): spp_cites_legislation() scope & language works ──
!all(res$cites_listings$is_current) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-legislations.R:47:5'): spp_cites_legislation() scope & language works ──
"Guinée" %in% res$cites_suspensions$geo_entity.name is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-legislations.R:54:5'): spp_eu_legislation() defaults works ───
nrow(res$eu_listings) (`actual`) not equal to 2 (`expected`).
`actual`: 0.0
`expected`: 2.0
── Failure ('test-legislations.R:55:5'): spp_eu_legislation() defaults works ───
"Namibia" %in% res$eu_decisions$geo_entity.name is not TRUE
`actual`: FALSE
`expected`: TRUE
── Error ('test-legislations.R:64:7'): spp_eu_legislation() raw mode works ─────
Error in `class(out) <- c("list", "spp_raw")`: attempt to set an attribute on NULL
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-legislations.R:63:5
2. │ └─cassette$call_block(...)
3. ├─testthat::expect_silent(...) at test-legislations.R:64:7
4. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
5. │ ├─testthat (local) .capture(...)
6. │ │ ├─withr::with_output_sink(...)
7. │ │ │ └─base::force(code)
8. │ │ ├─base::withCallingHandlers(...)
9. │ │ └─base::withVisible(code)
10. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
11. └─rcites::spp_eu_legislation(taxon_id = tx_id, raw = TRUE, verbose = FALSE)
── Failure ('test-legislations.R:89:5'): spp_cites_legislation() scope & lang works ──
!all(res$eu_listings$is_current) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-legislations.R:90:5'): spp_cites_legislation() scope & lang works ──
"Namibie" %in% res$eu_decisions$geo_entity.name is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-legislations.R:102:5'): spp_cites_legislation() batch mode works ──
unique(res$cites_listings$taxon_id) (`actual`) not identical to c(tx_id, tx_id2) (`expected`).
`actual` is NULL
`expected` is a character vector ('4521', '3210')
── Failure ('test-legislations.R:119:5'): spp_cites_legislation() batch mode works ──
unique(res$eu_listings$taxon_id) (`actual`) not identical to c(tx_id, tx_id2) (`expected`).
`actual` is NULL
`expected` is a character vector ('4521', '3210')
── Error ('test-references.R:16:5'): spp_references() raw mode ─────────────────
Error in `class(out) <- c("list", "spp_raw")`: attempt to set an attribute on NULL
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-references.R:15:3
2. │ └─cassette$call_block(...)
3. ├─testthat::expect_silent(...) at test-references.R:16:5
4. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
5. │ ├─testthat (local) .capture(...)
6. │ │ ├─withr::with_output_sink(...)
7. │ │ │ └─base::force(code)
8. │ │ ├─base::withCallingHandlers(...)
9. │ │ └─base::withVisible(code)
10. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
11. └─rcites::spp_references(taxon_id = tx_id, raw = TRUE, verbose = FALSE)
── Failure ('test-references.R:40:3'): spp_references() batch mode works ───────
unique(res$references$taxon_id) (`actual`) not identical to c(tx_id, tx_id2) (`expected`).
`actual` is NULL
`expected` is a character vector ('4521', '3210')
── Error ('test-references.R:45:5'): spp_references() raw batch mode works ─────
Error in `class(out) <- c("list", "spp_raw")`: attempt to set an attribute on NULL
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-references.R:44:3
2. │ └─cassette$call_block(...)
3. └─rcites::spp_references(...) at test-references.R:45:5
4. └─base::lapply(...)
5. └─rcites (local) FUN(X[[i]], ...)
── Error ('test-taxonconcept.R:12:5'): spp_taxonconcept() defaults work ────────
Error in `if (!pag) {
warning("Taxon not listed.")
return(NULL)
} else {
if (pag > 1) {
if (is.null(pages))
pages <- seq_len(pag)
else pages <- pages[pages <= pag]
if (!length(pages))
stop("Only page 1-", pag, " are available.")
if (length(pages) > 1) {
res <- rcites_autopagination(q_url, per_page, pages[-1L],
pag, token, verbose, ...)
tmp2 <- c(tmp$taxon_concepts, do.call(c, lapply(res,
function(x) x$taxon_concepts)))
}
else tmp2 <- tmp$taxon_concepts
}
else tmp2 <- tmp$taxon_concepts
if (raw) {
class(tmp2) <- c("list", "spp_raw")
return(tmp2)
}
else {
sp_nm <- c("synonyms", "higher_taxa", "common_names",
"cites_listing", "cites_listings", "accepted_names")
out <- list()
out$all_id <- rcites_taxonconcept_allentries(tmp2, sp_nm)
out$all_id$updated_at <- as.POSIXlt(out$all_id$updated_at,
format = "%Y-%m-%dT%H:%M:%OS")
out$all_id$active <- as.logical(out$all_id$active)
id <- which(out$all_id$active)
out$general <- out$all_id[out$all_id$active, ]
out$higher_taxa <- rcites_taxonconcept_higher_taxa(tmp2[id],
out$general$id)
out$accepted_names <- rcites_taxonconcept_names(tmp2[!id],
"accepted_names", out$all_id$id[!id])
out$common_names <- rcites_taxonconcept_names(tmp2[id],
"common_names", out$general$id)
out$synonyms <- rcites_taxonconcept_names(tmp2[id], "synonyms",
out$general$id)
if (taxonomy == "CITES") {
tmp_cit <- lapply(tmp2[id], function(x) x$cites_listing)
out$general$cites_listing <- unlist(lapply(tmp_cit,
rcites_null_to_na))
out$cites_listings <- rcites_taxonconcept_cites_listings(tmp2[id],
out$general$id)
}
class(out$general) <- class(out$all_id) <- c("tbl_df",
"tbl", "data.frame")
class(out) <- c("spp_taxon")
attr(out, "taxonomy") <- taxonomy
}
}`: argument is of length zero
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-taxonconcept.R:11:3
2. │ └─cassette$call_block(...)
3. ├─base::suppressMessages(res <- spp_taxonconcept(query_taxon = tx_nm)) at test-taxonconcept.R:12:5
4. │ └─base::withCallingHandlers(...)
5. └─rcites::spp_taxonconcept(query_taxon = tx_nm)
── Error ('test-taxonconcept.R:29:7'): spp_taxonconcept() raw mode works ───────
Error in `if (!pag) {
warning("Taxon not listed.")
return(NULL)
} else {
if (pag > 1) {
if (is.null(pages))
pages <- seq_len(pag)
else pages <- pages[pages <= pag]
if (!length(pages))
stop("Only page 1-", pag, " are available.")
if (length(pages) > 1) {
res <- rcites_autopagination(q_url, per_page, pages[-1L],
pag, token, verbose, ...)
tmp2 <- c(tmp$taxon_concepts, do.call(c, lapply(res,
function(x) x$taxon_concepts)))
}
else tmp2 <- tmp$taxon_concepts
}
else tmp2 <- tmp$taxon_concepts
if (raw) {
class(tmp2) <- c("list", "spp_raw")
return(tmp2)
}
else {
sp_nm <- c("synonyms", "higher_taxa", "common_names",
"cites_listing", "cites_listings", "accepted_names")
out <- list()
out$all_id <- rcites_taxonconcept_allentries(tmp2, sp_nm)
out$all_id$updated_at <- as.POSIXlt(out$all_id$updated_at,
format = "%Y-%m-%dT%H:%M:%OS")
out$all_id$active <- as.logical(out$all_id$active)
id <- which(out$all_id$active)
out$general <- out$all_id[out$all_id$active, ]
out$higher_taxa <- rcites_taxonconcept_higher_taxa(tmp2[id],
out$general$id)
out$accepted_names <- rcites_taxonconcept_names(tmp2[!id],
"accepted_names", out$all_id$id[!id])
out$common_names <- rcites_taxonconcept_names(tmp2[id],
"common_names", out$general$id)
out$synonyms <- rcites_taxonconcept_names(tmp2[id], "synonyms",
out$general$id)
if (taxonomy == "CITES") {
tmp_cit <- lapply(tmp2[id], function(x) x$cites_listing)
out$general$cites_listing <- unlist(lapply(tmp_cit,
rcites_null_to_na))
out$cites_listings <- rcites_taxonconcept_cites_listings(tmp2[id],
out$general$id)
}
class(out$general) <- class(out$all_id) <- c("tbl_df",
"tbl", "data.frame")
class(out) <- c("spp_taxon")
attr(out, "taxonomy") <- taxonomy
}
}`: argument is of length zero
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-taxonconcept.R:28:5
2. │ └─cassette$call_block(...)
3. ├─testthat::expect_silent(...) at test-taxonconcept.R:29:7
4. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
5. │ ├─testthat (local) .capture(...)
6. │ │ ├─withr::with_output_sink(...)
7. │ │ │ └─base::force(code)
8. │ │ ├─base::withCallingHandlers(...)
9. │ │ └─base::withVisible(code)
10. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
11. └─rcites::spp_taxonconcept(query_taxon = tx_nm, raw = TRUE, verbose = FALSE)
── Error ('test-taxonconcept.R:43:7'): spp_taxonconcept() CMS works ────────────
Error in `if (!pag) {
warning("Taxon not listed.")
return(NULL)
} else {
if (pag > 1) {
if (is.null(pages))
pages <- seq_len(pag)
else pages <- pages[pages <= pag]
if (!length(pages))
stop("Only page 1-", pag, " are available.")
if (length(pages) > 1) {
res <- rcites_autopagination(q_url, per_page, pages[-1L],
pag, token, verbose, ...)
tmp2 <- c(tmp$taxon_concepts, do.call(c, lapply(res,
function(x) x$taxon_concepts)))
}
else tmp2 <- tmp$taxon_concepts
}
else tmp2 <- tmp$taxon_concepts
if (raw) {
class(tmp2) <- c("list", "spp_raw")
return(tmp2)
}
else {
sp_nm <- c("synonyms", "higher_taxa", "common_names",
"cites_listing", "cites_listings", "accepted_names")
out <- list()
out$all_id <- rcites_taxonconcept_allentries(tmp2, sp_nm)
out$all_id$updated_at <- as.POSIXlt(out$all_id$updated_at,
format = "%Y-%m-%dT%H:%M:%OS")
out$all_id$active <- as.logical(out$all_id$active)
id <- which(out$all_id$active)
out$general <- out$all_id[out$all_id$active, ]
out$higher_taxa <- rcites_taxonconcept_higher_taxa(tmp2[id],
out$general$id)
out$accepted_names <- rcites_taxonconcept_names(tmp2[!id],
"accepted_names", out$all_id$id[!id])
out$common_names <- rcites_taxonconcept_names(tmp2[id],
"common_names", out$general$id)
out$synonyms <- rcites_taxonconcept_names(tmp2[id], "synonyms",
out$general$id)
if (taxonomy == "CITES") {
tmp_cit <- lapply(tmp2[id], function(x) x$cites_listing)
out$general$cites_listing <- unlist(lapply(tmp_cit,
rcites_null_to_na))
out$cites_listings <- rcites_taxonconcept_cites_listings(tmp2[id],
out$general$id)
}
class(out$general) <- class(out$all_id) <- c("tbl_df",
"tbl", "data.frame")
class(out) <- c("spp_taxon")
attr(out, "taxonomy") <- taxonomy
}
}`: argument is of length zero
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-taxonconcept.R:42:5
2. │ └─cassette$call_block(...)
3. └─rcites::spp_taxonconcept(...) at test-taxonconcept.R:43:7
── Error ('test-taxonconcept.R:54:7'): spp_taxonconcept() page selection works ──
Error in `if (!pag) {
warning("Taxon not listed.")
return(NULL)
} else {
if (pag > 1) {
if (is.null(pages))
pages <- seq_len(pag)
else pages <- pages[pages <= pag]
if (!length(pages))
stop("Only page 1-", pag, " are available.")
if (length(pages) > 1) {
res <- rcites_autopagination(q_url, per_page, pages[-1L],
pag, token, verbose, ...)
tmp2 <- c(tmp$taxon_concepts, do.call(c, lapply(res,
function(x) x$taxon_concepts)))
}
else tmp2 <- tmp$taxon_concepts
}
else tmp2 <- tmp$taxon_concepts
if (raw) {
class(tmp2) <- c("list", "spp_raw")
return(tmp2)
}
else {
sp_nm <- c("synonyms", "higher_taxa", "common_names",
"cites_listing", "cites_listings", "accepted_names")
out <- list()
out$all_id <- rcites_taxonconcept_allentries(tmp2, sp_nm)
out$all_id$updated_at <- as.POSIXlt(out$all_id$updated_at,
format = "%Y-%m-%dT%H:%M:%OS")
out$all_id$active <- as.logical(out$all_id$active)
id <- which(out$all_id$active)
out$general <- out$all_id[out$all_id$active, ]
out$higher_taxa <- rcites_taxonconcept_higher_taxa(tmp2[id],
out$general$id)
out$accepted_names <- rcites_taxonconcept_names(tmp2[!id],
"accepted_names", out$all_id$id[!id])
out$common_names <- rcites_taxonconcept_names(tmp2[id],
"common_names", out$general$id)
out$synonyms <- rcites_taxonconcept_names(tmp2[id], "synonyms",
out$general$id)
if (taxonomy == "CITES") {
tmp_cit <- lapply(tmp2[id], function(x) x$cites_listing)
out$general$cites_listing <- unlist(lapply(tmp_cit,
rcites_null_to_na))
out$cites_listings <- rcites_taxonconcept_cites_listings(tmp2[id],
out$general$id)
}
class(out$general) <- class(out$all_id) <- c("tbl_df",
"tbl", "data.frame")
class(out) <- c("spp_taxon")
attr(out, "taxonomy") <- taxonomy
}
}`: argument is of length zero
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-taxonconcept.R:53:5
2. │ └─cassette$call_block(...)
3. └─rcites::spp_taxonconcept(...) at test-taxonconcept.R:54:7
── Error ('test-taxonconcept.R:66:5'): spp_taxonconcept() updated_since works ──
Error in `if (!pag) {
warning("Taxon not listed.")
return(NULL)
} else {
if (pag > 1) {
if (is.null(pages))
pages <- seq_len(pag)
else pages <- pages[pages <= pag]
if (!length(pages))
stop("Only page 1-", pag, " are available.")
if (length(pages) > 1) {
res <- rcites_autopagination(q_url, per_page, pages[-1L],
pag, token, verbose, ...)
tmp2 <- c(tmp$taxon_concepts, do.call(c, lapply(res,
function(x) x$taxon_concepts)))
}
else tmp2 <- tmp$taxon_concepts
}
else tmp2 <- tmp$taxon_concepts
if (raw) {
class(tmp2) <- c("list", "spp_raw")
return(tmp2)
}
else {
sp_nm <- c("synonyms", "higher_taxa", "common_names",
"cites_listing", "cites_listings", "accepted_names")
out <- list()
out$all_id <- rcites_taxonconcept_allentries(tmp2, sp_nm)
out$all_id$updated_at <- as.POSIXlt(out$all_id$updated_at,
format = "%Y-%m-%dT%H:%M:%OS")
out$all_id$active <- as.logical(out$all_id$active)
id <- which(out$all_id$active)
out$general <- out$all_id[out$all_id$active, ]
out$higher_taxa <- rcites_taxonconcept_higher_taxa(tmp2[id],
out$general$id)
out$accepted_names <- rcites_taxonconcept_names(tmp2[!id],
"accepted_names", out$all_id$id[!id])
out$common_names <- rcites_taxonconcept_names(tmp2[id],
"common_names", out$general$id)
out$synonyms <- rcites_taxonconcept_names(tmp2[id], "synonyms",
out$general$id)
if (taxonomy == "CITES") {
tmp_cit <- lapply(tmp2[id], function(x) x$cites_listing)
out$general$cites_listing <- unlist(lapply(tmp_cit,
rcites_null_to_na))
out$cites_listings <- rcites_taxonconcept_cites_listings(tmp2[id],
out$general$id)
}
class(out$general) <- class(out$all_id) <- c("tbl_df",
"tbl", "data.frame")
class(out) <- c("spp_taxon")
attr(out, "taxonomy") <- taxonomy
}
}`: argument is of length zero
Backtrace:
▆
1. ├─vcr::use_cassette(...) at test-taxonconcept.R:65:3
2. │ └─cassette$call_block(...)
3. └─rcites::spp_taxonconcept(...) at test-taxonconcept.R:66:5
[ FAIL 28 | WARN 15 | SKIP 5 | PASS 42 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc