* using log directory ‘/home/hornik/tmp/CRAN_special_noSuggests/occCite.Rcheck’ * using R Under development (unstable) (2024-10-15 r87238) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc-14 (Debian 14.2.0-1) 14.2.0 GNU Fortran (Debian 14.2.0-1) 14.2.0 * running under: Debian GNU/Linux trixie/sid * 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 CRAN incoming feasibility ... [5s/7s] NOTE Maintainer: ‘Hannah L. Owens ’ Suggests or Enhances not in mainstream repositories: taxize * 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 executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘occCite’ can be installed ... [6s/6s] OK * checking package directory ... OK * checking for future file timestamps ... 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 ... [1s/1s] OK * checking whether the package can be loaded with stated dependencies ... [1s/1s] OK * checking whether the package can be unloaded cleanly ... [1s/1s] OK * checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK * checking whether the namespace can be unloaded cleanly ... [1s/1s] OK * checking loading without being on the library search path ... [1s/1s] 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/8s] OK * checking Rd files ... [0s/0s] OK * checking Rd metadata ... OK * checking Rd line widths ... 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 ... [1s/1s] 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 ... [3s/3s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [4s/11s] ERROR Running ‘testthat.R’ [4s/10s] 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 171 ] ══ Skipped tests (17) ══════════════════════════════════════════════════════════ • On CRAN (16): '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-occCitePrint.R:5:3', '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' • internet connection established (1): 'test-occCitation.R:115:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-taxonRectification.R:9:3'): functions on which it depends function as necessary ── Error in `loadNamespace(x)`: there is no package called 'taxize' Backtrace: ▆ 1. └─base::loadNamespace(x) at test-taxonRectification.R:9:3 2. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL) 3. └─base (local) withOneRestart(expr, restarts[[1L]]) 4. └─base (local) doWithOneRestart(return(expr), restart) ── Failure ('test-taxonRectification.R:45:3'): taxonRectification performs as expected ── testResult$`Best Match`[1] == "Buteo buteo harterti" is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-taxonRectification.R:46:3'): taxonRectification performs as expected ── testResult$`Searched Taxonomic Databases w/ Matches` == "National Center for Biotechnology Information" is not TRUE `actual`: FALSE `expected`: TRUE [ FAIL 3 | WARN 1 | SKIP 17 | PASS 171 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [8s/19s] OK * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [0s/0s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 1 NOTE