* using log directory 'd:/Rcompile/CRANpkg/local/4.5/skipTrack.Rcheck'
* using R Under development (unstable) (2025-01-18 r87593 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'skipTrack/DESCRIPTION' ... OK
* this is package 'skipTrack' version '0.1.0'
* 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 'skipTrack' 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 code 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 ... [0s] OK
* checking whether the package can be unloaded cleanly ... [1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s] 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 ... [4s] OK
* checking Rd files ... [1s] OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  skipTrack.diagnostics.Rd: genDiagnostic
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 ... [10s] ERROR
Running examples in 'skipTrack-Ex.R' failed
The error most likely occurred in:

> ### Name: skipTrack.diagnostics
> ### Title: skipTrack MCMC Diagnostics
> ### Aliases: skipTrack.diagnostics
> 
> ### ** Examples
> 
> #Simulated data
> simDat <- skipTrack.simulate(n = 100, skipProb = c(.7, .2, .1))
> 
> #Run model fit (should typically run with much more than 50 reps)
> modFit <- skipTrack.fit(Y = simDat$Y, cluster = simDat$cluster, chains = 2, reps = 50)
> 
> #Get diagnostics for cijs
> skipTrack.diagnostics(modFit, 'cijs')
Warning in genMCMCDiag::genDiagnostic(mcmcExt, method = method, distance = genMCMCDiag::hammingDist,  :
  this proximityMap ignores the argument distance.
Error in proximityMapF(mhDraws = mhDraws, distance = distance, verbose = verbose,  : 
  The chains must be numeric vectors in order to use the standard transformation.
Calls: skipTrack.diagnostics -> <Anonymous> -> proximityMapF
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [7s] ERROR
  Running 'testthat.R' [7s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(skipTrack)
  > 
  > test_check("skipTrack")
  -------------------------------------------
  SkipTrack Model Output
  -------------------------------------------
  Number of Observations:   62
  Number of Individuals:    10
  Dimension of Beta:        1
  Dimension of Gamma:       1
  -------------------------------------------
  Number of MCMC Chains:    2
  Model:                    skipTrack
  -------------------------------------------
  skipTrack.model S3 Object (also a list)
  
  NChains:    2
  Model Type: skipTrack[ FAIL 7 | WARN 7 | SKIP 0 | PASS 12 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-diagnostics.R:9:3'): skipTrack.diagnostics runs on all options ──
  Expected `skipTrack.diagnostics(foo, "Betas")` to run without any errors.
  i Actually got a <simpleError> with text:
    The chains must be numeric vectors in order to use the standard transformation.
  ── Failure ('test-diagnostics.R:10:3'): skipTrack.diagnostics runs on all options ──
  Expected `skipTrack.diagnostics(foo, "Gammas")` to run without any errors.
  i Actually got a <simpleError> with text:
    The chains must be numeric vectors in order to use the standard transformation.
  ── Failure ('test-diagnostics.R:11:3'): skipTrack.diagnostics runs on all options ──
  Expected `skipTrack.diagnostics(foo, "muis")` to run without any errors.
  i Actually got a <simpleError> with text:
    The chains must be numeric vectors in order to use the standard transformation.
  ── Failure ('test-diagnostics.R:12:3'): skipTrack.diagnostics runs on all options ──
  Expected `skipTrack.diagnostics(foo, "tauis")` to run without any errors.
  i Actually got a <simpleError> with text:
    The chains must be numeric vectors in order to use the standard transformation.
  ── Failure ('test-diagnostics.R:13:3'): skipTrack.diagnostics runs on all options ──
  Expected `skipTrack.diagnostics(foo, "cijs")` to run without any errors.
  i Actually got a <simpleError> with text:
    The chains must be numeric vectors in order to use the standard transformation.
  ── Error ('test-results.R:6:3'): results function runs ─────────────────────────
  Error in `proximityMapF(mhDraws = mhDraws, distance = distance, verbose = verbose, 
      ...)`: The chains must be numeric vectors in order to use the standard transformation.
  Backtrace:
      ▆
   1. └─skipTrack::skipTrack.results(foo, burnIn = 10) at test-results.R:6:3
   2.   └─base::lapply(...)
   3.     └─skipTrack (local) FUN(X[[i]], ...)
   4.       └─skipTrack::skipTrack.diagnostics(stFit = stFit, param)
   5.         └─genMCMCDiag::genDiagnostic(...)
   6.           └─genMCMCDiag (local) proximityMapF(...)
  ── Failure ('test-utils.R:9:3'): Utility functions do not throw errors ─────────
  Expected `summary(foo, burnIn = 20)` to run without any errors.
  i Actually got a <simpleError> with text:
    The chains must be numeric vectors in order to use the standard transformation.
  
  [ FAIL 7 | WARN 7 | SKIP 0 | PASS 12 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [71s] ERROR
Error(s) in re-building vignettes:
--- re-building 'skipTrack_intro.Rmd' using rmarkdown

Quitting from lines 122-123 [unnamed-chunk-6] (skipTrack_intro.Rmd)
Error: processing vignette 'skipTrack_intro.Rmd' failed with diagnostics:
The chains must be numeric vectors in order to use the standard transformation.
--- failed re-building 'skipTrack_intro.Rmd'

SUMMARY: processing the following file failed:
  'skipTrack_intro.Rmd'

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... [22s] OK
* checking HTML version of manual ... [6s] OK
* DONE
Status: 3 ERRORs, 1 NOTE