• using R Under development (unstable) (2025-01-19 r87600)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     Debian clang version 19.1.6 (1+b1)     Debian flang-new version 19.1.6 (1+b1)
• running under: Debian GNU/Linux trixie/sid
• using session charset: UTF-8
• checking for file ‘arealDB/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘arealDB’ version ‘0.6.3’
• 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 executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking serialization versions ... OK
• checking whether package ‘arealDB’ can be installed ... WARNING Found the following significant warnings:   Note: possible error in 'edit_matches(new = externalConcepts$label, ': unused argument (target = externalConcepts %>% select(has_broader, class)) See the install log for details. Information on the location(s) of code generating the ‘Note’s can be obtained by re-running with environment variable R_KEEP_PKG_SOURCE set to ‘yes’.
• checking package directory ... OK
• checking for future file timestamps ... OK
• checking ‘build’ directory ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
• checking for left-over files ... OK
• checking index information ... OK
• checking package subdirectories ... OK
• checking code files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... [3s/4s] OK
• checking whether the package can be loaded with stated dependencies ... [2s/3s] OK
• checking whether the package can be unloaded cleanly ... [2s/3s] OK
• checking whether the namespace can be loaded with stated dependencies ... [2s/3s] OK
• checking whether the namespace can be unloaded cleanly ... [3s/4s] OK
• checking loading without being on the library search path ... [3s/4s] OK
• checking whether startup messages can be suppressed ... [3s/4s] OK
• checking use of S3 registration ... OK
• checking dependencies in R code ... OK
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... [19s/25s] NOTE matchOntology: possible error in edit_matches(new =   externalConcepts$label, target = externalConcepts %>%   select(has_broader, class), source = dataseries, ontology = ontology,   matchDir = paste0(intPaths, "/meta/", type, "/"), verbose = verbose,   beep = beep): unused argument (target = externalConcepts %>%   select(has_broader, class))
• checking Rd files ... [0s/1s] OK
• checking Rd metadata ... OK
• checking Rd line widths ... OK
• checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors:   normGeometry.Rd: st_drivers   normTable.Rd: reorganise Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages.
• 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 installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [4s/5s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [15s/29s] ERROR   Running ‘testthat.R’ [15s/29s] Running the tests in ‘tests/testthat.R’ failed. Complete output:   > library(testthat)   >   > test_check("arealDB")   Loading required package: arealDB                                 [ FAIL 5 | WARN 1 | SKIP 4 | PASS 62 ]      ══ Skipped tests (4) ═══════════════════════════════════════════════════════════   • empty test (4): 'test_matchOntology.R:7:1', 'test_matchOntology.R:12:1',     'test_matchOntology.R:17:1', 'test_matchOntology.R:22:1'      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Error ('test_01_makeExampleDB.R:89:3'): make example DB until normGeometry ──   Error in `edit_matches(new = externalConcepts$label, target = externalConcepts %>%       select(has_broader, class), source = dataseries, ontology = ontology,       matchDir = paste0(intPaths, "/meta/", type, "/"), verbose = verbose,       beep = beep)`: unused argument (target = externalConcepts %>% select(has_broader, class))   Backtrace:       ▆    1. └─arealDB::makeExampleDB(until = "normGeometry", path = dbpath) at test_01_makeExampleDB.R:89:3    2. └─arealDB::normGeometry(update = TRUE, verbose = verbose)    3. └─arealDB::matchOntology(...)   ── Error ('test_01_makeExampleDB.R:99:3'): make example DB until normTable ─────   Error in `edit_matches(new = externalConcepts$label, target = externalConcepts %>%       select(has_broader, class), source = dataseries, ontology = ontology,       matchDir = paste0(intPaths, "/meta/", type, "/"), verbose = verbose,       beep = beep)`: unused argument (target = externalConcepts %>% select(has_broader, class))   Backtrace:       ▆    1. └─arealDB::makeExampleDB(until = "normTable", path = dbpath) at test_01_makeExampleDB.R:99:3    2. └─arealDB::normGeometry(update = TRUE, verbose = verbose)    3. └─arealDB::matchOntology(...)   ── Error ('test_06_normGeometry.R:16:3'): geometries can be normalised ─────────   Error in `edit_matches(new = externalConcepts$label, target = externalConcepts %>%       select(has_broader, class), source = dataseries, ontology = ontology,       matchDir = paste0(intPaths, "/meta/", type, "/"), verbose = verbose,       beep = beep)`: unused argument (target = externalConcepts %>% select(has_broader, class))   Backtrace:       ▆    1. └─arealDB::normGeometry(...) at test_06_normGeometry.R:16:3    2. └─arealDB::matchOntology(...)   ── Error ('test_07_normTable.R:13:3'): tables can be normalised (without matched variables) ──   Error in `edit_matches(new = externalConcepts$label, target = externalConcepts %>%       select(has_broader, class), source = dataseries, ontology = ontology,       matchDir = paste0(intPaths, "/meta/", type, "/"), verbose = verbose,       beep = beep)`: unused argument (target = externalConcepts %>% select(has_broader, class))   Backtrace:       ▆    1. └─arealDB::makeExampleDB(until = "normGeometry", path = dbpath) at test_07_normTable.R:13:3    2. └─arealDB::normGeometry(update = TRUE, verbose = verbose)    3. └─arealDB::matchOntology(...)   ── Error ('test_07_normTable.R:42:3'): tables can be normalised (with matched variables) ──   Error in `edit_matches(new = externalConcepts$label, target = externalConcepts %>%       select(has_broader, class), source = dataseries, ontology = ontology,       matchDir = paste0(intPaths, "/meta/", type, "/"), verbose = verbose,       beep = beep)`: unused argument (target = externalConcepts %>% select(has_broader, class))   Backtrace:       ▆    1. └─arealDB::makeExampleDB(until = "normGeometry", path = dbpath) at test_07_normTable.R:42:3    2. └─arealDB::normGeometry(update = TRUE, verbose = verbose)    3. └─arealDB::matchOntology(...)      [ FAIL 5 | WARN 1 | SKIP 4 | PASS 62 ]   Error: Test failures   Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [3s/4s] OK
• checking PDF version of manual ... [6s/8s] OK
• checking HTML version of manual ... [1s/1s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR, 1 WARNING, 2 NOTEs