• using R Under development (unstable) (2025-12-18 r89199)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     Debian clang version 21.1.7 (1)     Debian flang version 21.1.7 (1)
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8
• checking for file ‘Rdiagnosislist/DESCRIPTION’ ... OK
• this is package ‘Rdiagnosislist’ version ‘1.4.0’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [1s/1s] OK
• 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 ‘Rdiagnosislist’ can be installed ... OK See the install log for details.
• 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 ... [0s/1s] OK
• checking whether the package can be unloaded cleanly ... [0s/1s] OK
• checking whether the namespace can be loaded with stated dependencies ... [0s/1s] OK
• checking whether the namespace can be unloaded cleanly ... [0s/1s] OK
• checking loading without being on the library search path ... [0s/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 ... [16s/21s] OK
• checking Rd files ... [1s/1s] 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 ... [0s/0s] 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] ERROR Running examples in ‘Rdiagnosislist-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: addWordnet > ### Title: Use WordNet to assist concept database creation > ### Aliases: addWordnet > > ### ** Examples > > WORDNET <- data.table::data.table(cat = c('noun.body', 'noun.state'), + wordnetId = bit64::as.integer64('1', '2'), + synonyms = list(c('heart', 'pump', 'ticker'), + c('infection', 'infectious')), + parents = list('cardiovascular system', + 'pathologic process'), + adj = list('cardiac', 'infectious')) > # Add Wordnet synonyms to a concept database table > SNOMED <- sampleSNOMED() > CDB_TABLE <- description(c('Heart', 'Infection'), + include_synonyms = TRUE)[type == 'Synonym', + list(conceptId, term = paste0(' ', tolower(term), ' '))] > addWordnet(CDB_TABLE, 'noun.state', WORDNET) Adding categories for noun.state Error in `[.data.table`(MERGELINK_SYNGROUPS, , `:=`(OK, length(setdiff(conceptIds_WN[[1]], :   attempt access index 3/3 in VECTOR_ELT Calls: addWordnet -> [ -> [.data.table Execution halted
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [18s/23s] OK   Running ‘testthat.R’ [17s/23s]
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [14s/19s] OK
• checking PDF version of manual ... [6s/8s] OK
• checking HTML version of manual ... [4s/7s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR