* using log directory 'd:/Rcompile/CRANpkg/local/4.3/Rdiagnosislist.Rcheck' * using R version 4.3.3 (2024-02-29 ucrt) * using platform: x86_64-w64-mingw32 (64-bit) * R was compiled by gcc.exe (GCC) 12.3.0 GNU Fortran (GCC) 12.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'Rdiagnosislist/DESCRIPTION' ... OK * this is package 'Rdiagnosislist' version '1.3' * 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 hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'Rdiagnosislist' 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 R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... [1s] OK * checking whether the package can be loaded with stated dependencies ... [1s] OK * checking whether the package can be unloaded cleanly ... [1s] OK * checking whether the namespace can be loaded with stated dependencies ... [1s] OK * checking whether the namespace can be unloaded cleanly ... [1s] OK * checking loading without being on the library search path ... [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 ... [12s] 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 ... [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 ... [19s] ERROR Running examples in 'Rdiagnosislist-Ex.R' failed The error most likely occurred in: > ### Name: loadSNOMED > ### Title: Load SNOMED CT files from a folder(s) into R data.table objects > ### Aliases: loadSNOMED > > ### ** Examples > > # Create a TEST environment and load the sample dictionaries > TEST <- sampleSNOMED() > > # Export to temporary directory > exportSNOMEDenvir(TEST, tempdir()) NULL > > # Try to import using the loadSNOMED function > TEST2 <- loadSNOMED(tempdir(), active_only = FALSE) Attempting to load from D:\temp\2024_12_20_01_50_00_19051\RtmpInOPeZ Warning in sub(folder, "", thisfile) : TRE pattern compilation error 'Invalid back reference' Error in sub(folder, "", thisfile) : invalid regular expression 'D:\temp\2024_12_20_01_50_00_19051\RtmpInOPeZ', reason 'Invalid back reference' Calls: loadSNOMED -> message -> .makeMessage -> lapply -> sub Execution halted * checking for unstated dependencies in 'tests' ... OK * checking tests ... [30s] ERROR Running 'testthat.R' [29s] Running the tests in 'tests/testthat.R' failed. Complete output: > 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%, :, is.double, match, order, rank > 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 [ FAIL 2 | WARN 2 | SKIP 0 | PASS 124 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test_loadSNOMED.R:14:2'): Test exporting and reloading sample SNOMED dictionary ── Error in `sub(folder, "", thisfile)`: invalid regular expression 'D:\temp\2024_12_20_01_50_00_19051\RtmpshAIoE', reason 'Invalid back reference' Backtrace: ▆ 1. └─Rdiagnosislist::loadSNOMED(tempdir(), active_only = FALSE) at test_loadSNOMED.R:14:9 2. ├─base::message("Attempting to load ", sub(folder, "", thisfile)) 3. │ └─base::.makeMessage(..., domain = domain, appendLF = appendLF) 4. │ └─base::lapply(list(...), as.character) 5. └─base::sub(folder, "", thisfile) ── Error ('test_loadSNOMED.R:51:2'): Test exporting and reloading multiple files ── Error in `sub(folder, "", thisfile)`: invalid regular expression 'D:\temp\2024_12_20_01_50_00_19051\RtmpshAIoE/1', reason 'Invalid back reference' Backtrace: ▆ 1. └─Rdiagnosislist::loadSNOMED(...) at test_loadSNOMED.R:51:9 2. ├─base::message("Attempting to load ", sub(folder, "", thisfile)) 3. │ └─base::.makeMessage(..., domain = domain, appendLF = appendLF) 4. │ └─base::lapply(list(...), as.character) 5. └─base::sub(folder, "", thisfile) [ FAIL 2 | WARN 2 | SKIP 0 | PASS 124 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking re-building of vignette outputs ... [13s] ERROR Error(s) in re-building vignettes: --- re-building 'SNOMEDcodelists.Rmd' using rmarkdown Quitting from lines 79-98 [unnamed-chunk-1] (SNOMEDcodelists.Rmd) Error: processing vignette 'SNOMEDcodelists.Rmd' failed with diagnostics: invalid regular expression 'D:\temp\2024_12_20_01_50_00_19051\RtmpakVdg1', reason 'Invalid back reference' --- failed re-building 'SNOMEDcodelists.Rmd' --- re-building 'convertingAndCreatingCodelists.Rmd' using rmarkdown --- finished re-building 'convertingAndCreatingCodelists.Rmd' --- re-building 'creatingConceptDatabaseForNLP.Rmd' using rmarkdown --- finished re-building 'creatingConceptDatabaseForNLP.Rmd' --- re-building 'customHierarchy.Rmd' using rmarkdown --- finished re-building 'customHierarchy.Rmd' SUMMARY: processing the following file failed: 'SNOMEDcodelists.Rmd' Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... [19s] OK * checking HTML version of manual ... [10s] OK * DONE Status: 3 ERRORs