R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > require(testthat) Loading required package: testthat > require(Rdiagnosislist) Loading required package: Rdiagnosislist Loading required package: readxl Attaching package: 'Rdiagnosislist' The following object is masked from 'package:stats': decompose The following objects are masked from 'package:base': intersect, setdiff, union > require(bit64) Loading required package: bit64 Loading required package: bit Attaching package: 'bit' The following object is masked from 'package:base': xor Attaching package bit64 package:bit64 (c) 2011-2017 Jens Oehlschlaegel creators: integer64 runif64 seq : coercion: as.integer64 as.vector as.logical as.integer as.double as.character as.bitstring logical operator: ! & | xor != == < <= >= > arithmetic operator: + - * / %/% %% ^ math: sign abs sqrt log log2 log10 math: floor ceiling trunc round querying: is.integer64 is.vector [is.atomic} [length] format print str values: is.na is.nan is.finite is.infinite aggregation: any all min max range sum prod cumulation: diff cummin cummax cumsum cumprod access: length<- [ [<- [[ [[<- combine: c rep cbind rbind as.data.frame WARNING don't use as subscripts WARNING semantics differ from integer for more help type ?bit64 Attaching package: 'bit64' The following object is masked from 'package:utils': hashtab The following objects are masked from 'package:base': %in%, :, colSums, is.double, match, order, rank, rowSums > require(data.table) Loading required package: data.table Attaching package: 'data.table' The following object is masked from 'package:bit': setattr > > test_check("Rdiagnosislist") NAME NROW NCOL MB COLS 1: BODY 159 3 0 conceptId,term,laterality 2: BODY_LATERALITY 0 3 0 conceptId,laterality,nonlat_parentId 3: CAUSES 84 2 0 conceptId,term 4: FINDINGS 464 2 0 conceptId,term 5: LATERALITY 24 2 0 conceptId,term 6: MORPH 0 2 0 conceptId,term 7: OTHERCAUSE 36 3 0 conceptId,term,semType 8: OVERLAP 0 2 0 findingId,otherId 9: QUAL 2 2 0 conceptId,term 10: SEMTYPE 685 2 0 conceptId,semType 11: SEVERITY 0 2 0 conceptId,term 12: STAGE 0 2 0 conceptId,term 13: TRANSITIVE 5094 2 0 ancestorId,descendantId KEY 1: term 2: conceptId 3: term 4: term 5: term 6: term 7: term 8: otherId 9: term 10: conceptId 11: term 12: [NULL] 13: descendantId Total: 0MB using type_size SNOMED CT tables loaded into environment: NAME NROW NCOL MB 1: CONCEPT 509 5 0 2: DESCRIPTION 1596 9 0 3: EXTENDEDMAP 915 12 0 4: HISTORY 199 14 0 5: QUERY 1767 3 0 6: REFSET 428 5 0 7: RELATIONSHIP 1915 10 0 8: SIMPLEMAP 124 6 0 9: STATEDRELATIONSHIP 329 10 0 COLS 1: id,effectiveTime,active,moduleId,definitionStatusId 2: id,effectiveTime,active,moduleId,conceptId,languageCode,... 3: effectiveTime,active,moduleId,refsetId,referencedComponentId,mapGroup,... 4: OLDCONCEPTID,OLDCONCEPTSTATUS,NEWCONCEPTID,NEWCONCEPTSTATUS,PATH,ISAMBIGUOUS,... 5: supertypeId,subtypeId,provenance 6: effectiveTime,active,moduleId,refsetId,referencedComponentId 7: id,effectiveTime,active,moduleId,sourceId,destinationId,... 8: effectiveTime,active,moduleId,refsetId,referencedComponentId,mapTarget 9: id,effectiveTime,active,moduleId,sourceId,destinationId,... KEY 1: id 2: id 3: mapPriority,mapCategoryId,refsetId,referencedComponentId 4: NEWCONCEPTID,OLDCONCEPTID 5: supertypeId,subtypeId 6: refsetId,referencedComponentId 7: sourceId,typeId,active 8: refsetId,mapTarget,referencedComponentId 9: sourceId,typeId,active Total: 0MB using type_size Error in get(FILENAMES[thispattern == pattern]$table, envir = SNOMED, : object 'CONCEPT' not found Error in get(FILENAMES[thispattern == pattern]$table, envir = SNOMED, : object 'RELATIONSHIP' not found Error in get(FILENAMES[thispattern == pattern]$table, envir = SNOMED, : object 'SIMPLEMAP' not found Error in get(FILENAMES[thispattern == pattern]$table, envir = SNOMED, : object 'REFSET' not found SNOMED CT tables loaded into environment: NAME NROW NCOL MB 1: CONCEPT 509 5 0 2: DESCRIPTION 1596 9 0 3: EXTENDEDMAP 915 12 0 4: HISTORY 199 14 0 5: QUERY 1767 3 0 6: REFSET 428 5 0 7: RELATIONSHIP 1915 10 0 8: SIMPLEMAP 124 6 0 9: STATEDRELATIONSHIP 329 10 0 COLS 1: id,effectiveTime,active,moduleId,definitionStatusId 2: id,effectiveTime,active,moduleId,conceptId,languageCode,... 3: effectiveTime,active,moduleId,refsetId,referencedComponentId,mapGroup,... 4: OLDCONCEPTID,OLDCONCEPTSTATUS,NEWCONCEPTID,NEWCONCEPTSTATUS,PATH,ISAMBIGUOUS,... 5: supertypeId,subtypeId,provenance 6: effectiveTime,active,moduleId,refsetId,referencedComponentId 7: id,effectiveTime,active,moduleId,sourceId,destinationId,... 8: effectiveTime,active,moduleId,refsetId,referencedComponentId,mapTarget 9: id,effectiveTime,active,moduleId,sourceId,destinationId,... KEY 1: id 2: id 3: mapPriority,mapCategoryId,refsetId,referencedComponentId 4: NEWCONCEPTID,OLDCONCEPTID 5: supertypeId,subtypeId 6: refsetId,referencedComponentId 7: sourceId,typeId,active 8: refsetId,mapTarget,referencedComponentId 9: sourceId,typeId,active Total: 0MB using type_size Error in get(FILENAMES[thispattern == pattern]$table, envir = SNOMED, : object 'CONCEPT' not found Error in get(FILENAMES[thispattern == pattern]$table, envir = SNOMED, : object 'SIMPLEMAP' not found Error in get(FILENAMES[thispattern == pattern]$table, envir = SNOMED, : object 'REFSET' not found [ FAIL 0 | WARN 2 | SKIP 0 | PASS 141 ] [ FAIL 0 | WARN 2 | SKIP 0 | PASS 141 ] > > proc.time() user system elapsed 12.00 2.87 14.87