* using log directory 'd:/Rcompile/CRANpkg/local/4.5/occCite.Rcheck' * using R Under development (unstable) (2025-03-11 r87944 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'occCite/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'occCite' version '0.5.9' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'occCite' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... [2s] OK * checking whether the package can be loaded with stated dependencies ... [2s] OK * checking whether the package can be unloaded cleanly ... [2s] OK * checking whether the namespace can be loaded with stated dependencies ... [1s] OK * checking whether the namespace can be unloaded cleanly ... [2s] OK * checking loading without being on the library search path ... [2s] OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [8s] OK * checking Rd files ... [1s] OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of 'data' directory ... OK * checking data for non-ASCII characters ... [2s] OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... [6s] OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... [51s] ERROR Running 'testthat.R' [51s] Running the tests in 'tests/testthat.R' failed. Complete output: > library(testthat) > library(occCite) > > test_check("occCite") OccCite query occurred on: 20 June, 2024 User query type: User-supplied list of taxa. Sources for taxonomic rectification: GBIF Backbone Taxonomy Taxonomic cleaning results: Input Name Best Match Taxonomic Databases w/ Matches 1 Protea cynaroides Protea cynaroides (L.) L. GBIF Backbone Taxonomy Sources for occurrence data: gbif, bien Species Occurrences Sources 1 Protea cynaroides (L.) L. 2334 17 GBIF dataset DOIs: Species GBIF Access Date GBIF DOI 1 Protea cynaroides (L.) L. 2022-03-02 10.15468/dl.ztbx8c OccCite query occurred on: 20 June, 2024 User query type: User-supplied list of taxa. Sources for taxonomic rectification: GBIF Backbone Taxonomy Taxonomic cleaning results: Input Name Best Match Taxonomic Databases w/ Matches 1 Protea cynaroides Protea cynaroides (L.) L. GBIF Backbone Taxonomy Sources for occurrence data: gbif Species Occurrences Sources 1 Protea cynaroides (L.) L. 2189 13 GBIF dataset DOIs: Species GBIF Access Date GBIF DOI 1 Protea cynaroides (L.) L. 2022-03-02 10.15468/dl.ztbx8c OccCite query occurred on: 20 June, 2024 User query type: User-supplied list of taxa. Sources for taxonomic rectification: GBIF Backbone Taxonomy Taxonomic cleaning results: Input Name Best Match Taxonomic Databases w/ Matches 1 Protea cynaroides Protea cynaroides (L.) L. GBIF Backbone Taxonomy Sources for occurrence data: bien Species Occurrences Sources 1 Protea cynaroides (L.) L. 145 4 [ FAIL 3 | WARN 1 | SKIP 17 | PASS 123 ] ══ Skipped tests (17) ══════════════════════════════════════════════════════════ • On CRAN (15): 'test-GBIFLoginManager.R:6:3', 'test-GBIFLoginManager.R:19:3', 'test-GBIFtableCleanup.R:6:3', 'test-gbifRetriever.R:6:3', 'test-gbifRetriever.R:29:3', 'test-getBIENpoints.R:6:3', 'test-getBIENpoints.R:28:3', 'test-getGBIFpoints.R:6:3', 'test-getGBIFpoints.R:24:3', 'test-occCitation.R:26:3', 'test-prevGBIFdownload.R:6:3', 'test-prevGBIFdownload.R:34:3', 'test-tabGBIF.R:9:3', 'test-tabGBIF.R:24:3', 'test-tabGBIF.R:48:3' • empty test (1): 'test-occCitePrint.R:4:1' • internet connection established (1): 'test-occCitation.R:115:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-studyTaxonList.R:17:3'): studyTaxonList works with a phylogeny ── Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached [resolver.globalnames.org]: SSL/TLS connection timeout Backtrace: ▆ 1. ├─testthat::skip_if(httr::http_error("https://resolver.globalnames.org/data_sources.json")) at test-studyTaxonList.R:17:3 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) 11. └─curl:::raise_libcurl_error(...) ── Error ('test-studyTaxonList.R:52:3'): studyTaxonList works with a vector of species ── Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached [resolver.globalnames.org]: SSL/TLS connection timeout Backtrace: ▆ 1. ├─testthat::skip_if(httr::http_error("https://resolver.globalnames.org/data_sources.json")) at test-studyTaxonList.R:52:3 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) 11. └─curl:::raise_libcurl_error(...) ── Error ('test-taxonRectification.R:31:3'): taxonRectification performs as expected ── Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached [resolver.globalnames.org]: SSL/TLS connection timeout Backtrace: ▆ 1. ├─testthat::skip_if(httr::http_error("https://resolver.globalnames.org/data_sources.json")) at test-taxonRectification.R:31:3 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) 11. └─curl:::raise_libcurl_error(...) [ FAIL 3 | WARN 1 | SKIP 17 | PASS 123 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [35s] OK * checking PDF version of manual ... [21s] OK * checking HTML version of manual ... [3s] OK * DONE Status: 1 ERROR