• 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 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 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