• 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 See the install log for details.
• 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 ... [17s] 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_11_13_01_50_00_32639\Rtmp0u5ytk Warning in sub(folder, "", thisfile) :   TRE pattern compilation error 'Invalid back reference' Error in sub(folder, "", thisfile) :   invalid regular expression 'D:\temp\2024_11_13_01_50_00_32639\Rtmp0u5ytk', 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' [30s] 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_11_13_01_50_00_32639\RtmpaujDz0', 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_11_13_01_50_00_32639\RtmpaujDz0/1', 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_11_13_01_50_00_32639\RtmpOoeIrf', 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 ... [9s] OK
• DONE

Status: 3 ERRORs