Last updated on 2021-10-22 17:51:07 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.5.0 | 10.34 | 226.08 | 236.42 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.5.0 | 8.60 | 167.70 | 176.30 | OK | |
| r-devel-linux-x86_64-fedora-clang | 0.5.0 | 229.00 | NOTE | |||
| r-devel-linux-x86_64-fedora-gcc | 0.5.0 | 213.64 | NOTE | |||
| r-devel-windows-x86_64 | 0.5.0 | 21.00 | 448.00 | 469.00 | OK | |
| r-devel-windows-x86_64-gcc10-UCRT | 0.5.0 | ERROR | ||||
| r-patched-linux-x86_64 | 0.5.0 | 16.72 | 224.67 | 241.39 | OK | |
| r-patched-solaris-x86 | 0.5.0 | 233.00 | ERROR | |||
| r-release-linux-x86_64 | 0.5.0 | 10.72 | 225.91 | 236.63 | OK | |
| r-release-macos-arm64 | 0.4.9 | NOTE | ||||
| r-release-macos-x86_64 | 0.5.0 | NOTE | ||||
| r-release-windows-ix86+x86_64 | 0.5.0 | 18.00 | 456.00 | 474.00 | OK | |
| r-oldrel-macos-x86_64 | 0.5.0 | NOTE | ||||
| r-oldrel-windows-ix86+x86_64 | 0.5.0 | 20.00 | 359.00 | 379.00 | OK |
Version: 0.5.0
Check: data for non-ASCII characters
Result: NOTE
Note: found 6 marked UTF-8 strings
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-solaris-x86, r-release-macos-x86_64, r-oldrel-macos-x86_64
Version: 0.5.0
Check: package dependencies
Result: ERROR
Package required but not available: 'taxize'
See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Flavor: r-devel-windows-x86_64-gcc10-UCRT
Version: 0.5.0
Check: examples
Result: ERROR
Running examples in ‘occCite-Ex.R’ failed
The error most likely occurred in:
> ### Name: studyTaxonList
> ### Title: Study Taxon List
> ### Aliases: studyTaxonList
>
> ### ** Examples
>
> ## Inputting a vector of taxon names
> studyTaxonList(
+ x = c(
+ "Buteo buteo",
+ "Buteo buteo hartedi",
+ "Buteo japonicus"
+ ),
+ datasources = c("National Center for Biotechnology Information")
+ )
Error in curl::curl_fetch_memory(url, handle = handle) :
SSL certificate problem: certificate has expired
Calls: studyTaxonList ... request_fetch -> request_fetch.write_memory -> <Anonymous>
Execution halted
Flavor: r-patched-solaris-x86
Version: 0.5.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [67s/182s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(occCite)
>
> test_check("occCite")
[1] "NOTE: 1 BIEN dataset(s) for Protea cynaroides is/are missing citation data. Key(s) missing citations are: 280. Source(s) are identified as: MO."
OccCite query occurred on: 24 November, 2020
User query type: User-supplied list of taxa.
Sources for taxonomic rectification: NCBI
Taxonomic cleaning results:
Input Name Best Match Taxonomic Databases w/ Matches
1 Protea cynaroides Protea cynaroides NCBI
Sources for occurrence data: gbif, bien
Species Occurrences Sources
1 Protea cynaroides 1293 17
GBIF dataset DOIs:
Species GBIF Access Date GBIF DOI
1 Protea cynaroides 2020-11-23 10.15468/dl.2449qy
OccCite query occurred on: 24 November, 2020
User query type: User-supplied list of taxa.
Sources for taxonomic rectification: NCBI
Taxonomic cleaning results:
Input Name Best Match Taxonomic Databases w/ Matches
1 Protea cynaroides Protea cynaroides NCBI
Sources for occurrence data: gbif
Species Occurrences Sources
1 Protea cynaroides 1145 12
GBIF dataset DOIs:
Species GBIF Access Date GBIF DOI
1 Protea cynaroides 2020-11-23 10.15468/dl.2449qy
OccCite query occurred on: 24 November, 2020
User query type: User-supplied list of taxa.
Sources for taxonomic rectification: NCBI
Taxonomic cleaning results:
Input Name Best Match Taxonomic Databases w/ Matches
1 Protea cynaroides Protea cynaroides NCBI
Sources for occurrence data: bien
Species Occurrences Sources
1 Protea cynaroides 148 5
══ Skipped tests ═══════════════════════════════════════════════════════════════
• GBIF Login information not available (1)
• On CRAN (14)
══ Failed tests ════════════════════════════════════════════════════════════════
── Error (test-occCitePrint.R:8:1): (code run outside of `test_that()`) ────────
Error in `curl::curl_fetch_memory(url, handle = handle)`: SSL certificate problem: certificate has expired
Backtrace:
█
1. └─occCite::studyTaxonList(x = tree, datasources = "GBIF Backbone Taxonomy") test-occCitePrint.R:8:0
2. ├─base::withCallingHandlers(...)
3. └─occCite::taxonRectification(taxName = targets[[i]], datasources = datasources)
4. ├─httr::http_error("https://resolver.globalnames.org/data_sources.json")
5. └─httr:::http_error.character("https://resolver.globalnames.org/data_sources.json")
6. ├─httr::http_error(HEAD(x, ...))
7. └─httr::HEAD(x, ...)
8. └─httr:::request_perform(req, hu$handle$handle)
9. ├─httr:::request_fetch(req$output, req$url, handle)
10. └─httr:::request_fetch.write_memory(req$output, req$url, handle)
11. └─curl::curl_fetch_memory(url, handle = handle)
── Error (test-studyTaxonList.R:16:3): studyTaxonList works with a phylogeny ───
Error in `curl::curl_fetch_memory(url, handle = handle)`: SSL certificate problem: certificate has expired
Backtrace:
█
1. ├─testthat::skip_if(httr::http_error("https://resolver.globalnames.org/data_sources.json")) test-studyTaxonList.R:16:2
2. │ └─base::isTRUE(condition)
3. ├─httr::http_error("https://resolver.globalnames.org/data_sources.json")
4. └─httr:::http_error.character("https://resolver.globalnames.org/data_sources.json")
5. ├─httr::http_error(HEAD(x, ...))
6. └─httr::HEAD(x, ...)
7. └─httr:::request_perform(req, hu$handle$handle)
8. ├─httr:::request_fetch(req$output, req$url, handle)
9. └─httr:::request_fetch.write_memory(req$output, req$url, handle)
10. └─curl::curl_fetch_memory(url, handle = handle)
── Error (test-studyTaxonList.R:48:3): studyTaxonList works with a vector of species ──
Error in `curl::curl_fetch_memory(url, handle = handle)`: SSL certificate problem: certificate has expired
Backtrace:
█
1. ├─testthat::skip_if(httr::http_error("https://resolver.globalnames.org/data_sources.json")) test-studyTaxonList.R:48:2
2. │ └─base::isTRUE(condition)
3. ├─httr::http_error("https://resolver.globalnames.org/data_sources.json")
4. └─httr:::http_error.character("https://resolver.globalnames.org/data_sources.json")
5. ├─httr::http_error(HEAD(x, ...))
6. └─httr::HEAD(x, ...)
7. └─httr:::request_perform(req, hu$handle$handle)
8. ├─httr:::request_fetch(req$output, req$url, handle)
9. └─httr:::request_fetch.write_memory(req$output, req$url, handle)
10. └─curl::curl_fetch_memory(url, handle = handle)
── Error (test-taxonRectification.R:6:3): functions on which it depends function as necessary ──
Error in `curl::curl_fetch_memory(url, handle = handle)`: SSL certificate problem: certificate has expired
Backtrace:
█
1. ├─testthat::skip_if(httr::http_error("https://resolver.globalnames.org/data_sources.json")) test-taxonRectification.R:6:2
2. │ └─base::isTRUE(condition)
3. ├─httr::http_error("https://resolver.globalnames.org/data_sources.json")
4. └─httr:::http_error.character("https://resolver.globalnames.org/data_sources.json")
5. ├─httr::http_error(HEAD(x, ...))
6. └─httr::HEAD(x, ...)
7. └─httr:::request_perform(req, hu$handle$handle)
8. ├─httr:::request_fetch(req$output, req$url, handle)
9. └─httr:::request_fetch.write_memory(req$output, req$url, handle)
10. └─curl::curl_fetch_memory(url, handle = handle)
── Error (test-taxonRectification.R:29:3): taxonRectification performs as expected ──
Error in `curl::curl_fetch_memory(url, handle = handle)`: SSL certificate problem: certificate has expired
Backtrace:
█
1. ├─testthat::skip_if(httr::http_error("https://resolver.globalnames.org/data_sources.json")) test-taxonRectification.R:29:2
2. │ └─base::isTRUE(condition)
3. ├─httr::http_error("https://resolver.globalnames.org/data_sources.json")
4. └─httr:::http_error.character("https://resolver.globalnames.org/data_sources.json")
5. ├─httr::http_error(HEAD(x, ...))
6. └─httr::HEAD(x, ...)
7. └─httr:::request_perform(req, hu$handle$handle)
8. ├─httr:::request_fetch(req$output, req$url, handle)
9. └─httr:::request_fetch.write_memory(req$output, req$url, handle)
10. └─curl::curl_fetch_memory(url, handle = handle)
[ FAIL 5 | WARN 0 | SKIP 15 | PASS 147 ]
Error: Test failures
Execution halted
Flavor: r-patched-solaris-x86
Version: 0.4.9
Check: data for non-ASCII characters
Result: NOTE
Note: found 6 marked UTF-8 strings
Flavor: r-release-macos-arm64