Last updated on 2025-08-23 11:49:23 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-fedora-gcc | 1.0.0 | 112.49 | OK | |||
| r-release-macos-x86_64 | 1.0.0 | 72.00 | ERROR | |||
| r-oldrel-macos-x86_64 | 1.0.0 | 83.00 | ERROR |
Version: 1.0.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(letsRept)
letsRept 1.0.0 loaded 🦎 🐍 🐊 🐢
Please cite both letsRept and The Reptile Database when using this package.
Run citation("letsRept") for details.
>
> test_check("letsRept")
objc[48190]: +[NSNumber initialize] may have been in progress in another thread when fork() was called.
objc[48190]: +[NSNumber initialize] may have been in progress in another thread when fork() was called. We cannot safely call it or ignore it in the fork() child process. Crashing instead. Set a breakpoint on objc_initializeAfterForkError to debug.
objc[48188]: +[NSNumber initialize] may have been in progress in another thread when fork() was called.
objc[48188]: +[NSNumber initialize] may have been in progress in another thread when fork() was called. We cannot safely call it or ignore it in the fork() child process. Crashing instead. Set a breakpoint on objc_initializeAfterForkError to debug.
objc[48300]: +[NSNumber initialize] may have been in progress in another thread when fork() was called.
objc[48300]: +[NSNumber initialize] may have been in progress in another thread when fork() was called. We cannot safely call it or ignore it in the fork() child process. Crashing instead. Set a breakpoint on objc_initializeAfterForkError to debug.
objc[48299]: +[NSNumber initialize] may have been in progress in another thread when fork() was called.
objc[48299]: +[NSNumber initialize] may have been in progress in another thread when fork() was called. We cannot safely call it or ignore it in the fork() child process. Crashing instead. Set a breakpoint on objc_initializeAfterForkError to debug.
col1 col2
-----------
[ FAIL 2 | WARN 3 | SKIP 7 | PASS 3 ]
══ Skipped tests (7) ═══════════════════════════════════════════════════════════
• On CRAN (7): 'test-reptAdvancedSearch.R:2:3', 'test-reptCompare.R:2:3',
'test-reptRefs.R:2:3', 'test-reptSearch.R:2:3', 'test-reptSpecies.R:2:3',
'test-reptStats.R:2:3', 'test-reptSynonyms.R:2:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-reptSplitCheck.R:13:3'): reptSplitCheck returns expected output ──
nrow(result) is not strictly more than 0. Difference: 0
── Error ('test-reptSync.R:4:3'): reptSync returns expected output ─────────────
Error in `if (nrow(synSample) > 0) {
ambiguity_results <- safeParallel(1:nrow(synSample), FUN = function(i) {
spp_syn <- reptSynonyms(reptSpecies(synSample$url[i],
getLink = TRUE, showProgress = FALSE, cores = cores),
cores = cores, showProgress = FALSE)
synonyms <- spp_syn$species[synSample$query[i] == spp_syn$synonyms]
if (length(synonyms) == 1) {
RDB_new <- synonyms
status_new <- "updated"
}
else if (length(synonyms) > 1) {
RDB_new <- paste(synonyms, collapse = "; ")
status_new <- "ambiguous"
}
else {
RDB_new <- "not_found"
status_new <- "not_found"
}
list(query = synSample$query[i], RDB_new = RDB_new, status_new = status_new)
}, cores = cores, showProgress = showProgress)
ambiguity_df <- do.call(rbind, lapply(ambiguity_results,
function(res) {
data.frame(query = res$query, RDB = res$RDB_new,
status = res$status_new, stringsAsFactors = FALSE)
}))
for (i in 1:nrow(ambiguity_df)) {
df$RDB[df$query == ambiguity_df$query[i]] <- ambiguity_df$RDB[i]
df$status[df$query == ambiguity_df$query[i]] <- ambiguity_df$status[i]
}
}`: argument is of length zero
Backtrace:
▆
1. └─letsRept::reptSync(x = query, cores = 2, showProgress = FALSE) at test-reptSync.R:4:3
[ FAIL 2 | WARN 3 | SKIP 7 | PASS 3 ]
Error: Test failures
Execution halted
Flavor: r-release-macos-x86_64
Version: 1.0.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
Error in saveRDS(list(base = base, value = ret0), dest) :
error writing to connection
Calls: <Anonymous> -> rownames -> %||% -> <Anonymous> -> saveRDS
Execution halted
Flavor: r-release-macos-x86_64
Version: 1.0.0
Check: PDF version of manual
Result: WARN
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Flavor: r-release-macos-x86_64
Version: 1.0.0
Check: PDF version of manual without index
Result: ERROR
Re-running with no redirection of stdout/stderr.
Flavor: r-release-macos-x86_64
Version: 1.0.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(letsRept)
letsRept 1.0.0 loaded 🦎 🐍 🐊 🐢
Please cite both letsRept and The Reptile Database when using this package.
Run citation("letsRept") for details.
>
> test_check("letsRept")
objc[10882]: +[NSNumber initialize] may have been in progress in another thread when fork() was called.
objc[10882]: +[NSNumber initialize] may have been in progress in another thread when fork() was called. We cannot safely call it or ignore it in the fork() child process. Crashing instead. Set a breakpoint on objc_initializeAfterForkError to debug.
objc[10881]: +[NSNumber initialize] may have been in progress in another thread when fork() was called.
objc[10881]: +[NSNumber initialize] may have been in progress in another thread when fork() was called. We cannot safely call it or ignore it in the fork() child process. Crashing instead. Set a breakpoint on objc_initializeAfterForkError to debug.
objc[10892]: +[NSNumber initialize] may have been in progress in another thread when fork() was called.
objc[10892]: +[NSNumber initialize] may have been in progress in another thread when fork() was called. We cannot safely call it or ignore it in the fork() child process. Crashing instead. Set a breakpoint on objc_initializeAfterForkError to debug.
objc[10893]: +[NSNumber initialize] may have been in progress in another thread when fork() was called.
objc[10893]: +[NSNumber initialize] may have been in progress in another thread when fork() was called. We cannot safely call it or ignore it in the fork() child process. Crashing instead. Set a breakpoint on objc_initializeAfterForkError to debug.
col1 col2
-----------
[ FAIL 2 | WARN 3 | SKIP 7 | PASS 3 ]
══ Skipped tests (7) ═══════════════════════════════════════════════════════════
• On CRAN (7): 'test-reptAdvancedSearch.R:2:3', 'test-reptCompare.R:2:3',
'test-reptRefs.R:2:3', 'test-reptSearch.R:2:3', 'test-reptSpecies.R:2:3',
'test-reptStats.R:2:3', 'test-reptSynonyms.R:2:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-reptSplitCheck.R:13:3'): reptSplitCheck returns expected output ──
nrow(result) is not strictly more than 0. Difference: 0
── Error ('test-reptSync.R:4:3'): reptSync returns expected output ─────────────
Error in `if (nrow(synSample) > 0) {
ambiguity_results <- safeParallel(1:nrow(synSample), FUN = function(i) {
spp_syn <- reptSynonyms(reptSpecies(synSample$url[i],
getLink = TRUE, showProgress = FALSE, cores = cores),
cores = cores, showProgress = FALSE)
synonyms <- spp_syn$species[synSample$query[i] == spp_syn$synonyms]
if (length(synonyms) == 1) {
RDB_new <- synonyms
status_new <- "updated"
}
else if (length(synonyms) > 1) {
RDB_new <- paste(synonyms, collapse = "; ")
status_new <- "ambiguous"
}
else {
RDB_new <- "not_found"
status_new <- "not_found"
}
list(query = synSample$query[i], RDB_new = RDB_new, status_new = status_new)
}, cores = cores, showProgress = showProgress)
ambiguity_df <- do.call(rbind, lapply(ambiguity_results,
function(res) {
data.frame(query = res$query, RDB = res$RDB_new,
status = res$status_new, stringsAsFactors = FALSE)
}))
for (i in 1:nrow(ambiguity_df)) {
df$RDB[df$query == ambiguity_df$query[i]] <- ambiguity_df$RDB[i]
df$status[df$query == ambiguity_df$query[i]] <- ambiguity_df$status[i]
}
}`: argument is of length zero
Backtrace:
▆
1. └─letsRept::reptSync(x = query, cores = 2, showProgress = FALSE) at test-reptSync.R:4:3
[ FAIL 2 | WARN 3 | SKIP 7 | PASS 3 ]
Error: Test failures
Execution halted
Flavor: r-oldrel-macos-x86_64
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