• using R Under development (unstable) (2025-12-21 r89216)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     Debian clang version 21.1.7 (1)     Debian flang version 21.1.7 (1)
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8
• checking for file ‘tna/DESCRIPTION’ ... OK
• this is package ‘tna’ version ‘1.1.0’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [2s/3s] OK
• 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 executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking whether package ‘tna’ can be installed ... WARNING Found the following significant warnings:   Warning: namespace ‘seqHMM’ is not available and has been replaced See the install log for details.
• checking package directory ... OK
• checking for future file timestamps ... 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/1s] OK
• checking whether the package can be loaded with stated dependencies ... [0s/1s] OK
• checking whether the package can be unloaded cleanly ... [0s/1s] OK
• checking whether the namespace can be loaded with stated dependencies ... [0s/1s] OK
• checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
• checking loading without being on the library search path ... [1s/1s] OK
• checking whether startup messages can be suppressed ... [1s/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 ... [19s/24s] OK
• checking Rd files ... [1s/1s] OK
• checking Rd metadata ... OK
• checking Rd line widths ... 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/1s] 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 ... [7s/8s] ERROR Running examples in ‘tna-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: cliques > ### Title: Identify Cliques in a Transition Network > ### Aliases: cliques cliques.tna cliques.group_tna > > ### ** Examples > > model <- tna(group_regulation) > > # Find 2-cliques (dyads) > cliq <- cliques(model, size = 2) > > model <- group_tna(engagement_mmm) Error in `[.data.table`(out, , `:=`(ll, logSumExp(log_alpha[time == time[.N]])), :   attempt access index 6/6 in VECTOR_ELT Calls: group_tna ... posterior_probs -> posterior_probs.mhmm -> [ -> [.data.table Execution halted
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [6s/6s] ERROR   Running ‘testthat.R’ [5s/6s] Running the tests in ‘tests/testthat.R’ failed. Complete output:   > suppressPackageStartupMessages(library("tna"))   > library("testthat")      Attaching package: 'testthat'      The following object is masked from 'package:tna':          compare      >   > test_check("tna")   Error in `source_dir()`:   ! Failed to evaluate './helper-mock.R'.   Caused by error in `[.data.table`:   ! attempt access index 6/6 in VECTOR_ELT   Backtrace:        ▆     1. ├─testthat::test_check("tna")     2. │ └─testthat::test_dir(...)     3. │ └─testthat:::test_files(...)     4. │ └─testthat:::test_files_serial(...)     5. │ └─testthat:::test_files_setup_state(...)     6. │ └─testthat::source_test_helpers(".", env)     7. │ └─testthat::source_dir(path, "^helper.*\\.[rR]$", env = env, wrap = FALSE)     8. │ └─base::lapply(...)     9. │ └─testthat (local) FUN(X[[i]], ...)    10. │ └─testthat::source_file(...)    11. │ ├─base::withCallingHandlers(...)    12. │ └─base::eval(exprs, env)    13. │ └─base::eval(exprs, env)    14. │ └─tna::group_tna(engagement_mmm) at ./helper-mock.R:47:1    15. │ ├─tna::group_model(x = x, type = "relative", ...)    16. │ └─tna:::group_model.mhmm(x = x, type = "relative", ...)    17. │ ├─tna:::group_model.default(...)    18. │ │ └─group %m% seq_len(nrow(x))    19. │ ├─base::summary(x)    20. │ └─seqHMM:::summary.mhmm(x)    21. │ └─seqHMM::posterior_cluster_probabilities(object)    22. │ ├─seqHMM::posterior_probs(x)    23. │ └─seqHMM:::posterior_probs.mhmm(x)    24. │ ├─...[]    25. │ └─data.table:::`[.data.table`(...)    26. └─base::.handleSimpleError(...)    27. └─testthat (local) h(simpleError(msg, call))    28. └─cli::cli_abort(...)    29. └─rlang::abort(...)   Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [117s/152s] ERROR Error(s) in re-building vignettes:   ... --- re-building ‘communities_and_cliques.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘communities_and_cliques.Rmd’ --- re-building ‘complete_tutorial.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘complete_tutorial.Rmd’ --- re-building ‘grouped_sequences.Rmd’ using rmarkdown Quitting from grouped_sequences.Rmd:74-76 [unnamed-chunk-5] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `[.data.table`: ! attempt access index 6/6 in VECTOR_ELT --- Backtrace:      ▆   1. ├─tna::group_model(engagement_mmm)   2. └─tna:::group_model.mhmm(engagement_mmm)   3. ├─tna:::group_model.default(...)   4. │ └─group %m% seq_len(nrow(x))   5. ├─base::summary(x)   6. └─seqHMM:::summary.mhmm(x)   7. └─seqHMM::posterior_cluster_probabilities(object)   8. ├─seqHMM::posterior_probs(x)   9. └─seqHMM:::posterior_probs.mhmm(x)  10. ├─...[]  11. └─data.table:::`[.data.table`(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'grouped_sequences.Rmd' failed with diagnostics: attempt access index 6/6 in VECTOR_ELT --- failed re-building ‘grouped_sequences.Rmd’ --- re-building ‘prepare_data.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘prepare_data.Rmd’ --- re-building ‘tna.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘tna.Rmd’ SUMMARY: processing the following file failed:   ‘grouped_sequences.Rmd’ Error: Vignette re-building failed. Execution halted
• checking PDF version of manual ... [10s/13s] OK
• checking HTML version of manual ... [12s/16s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 3 ERRORs, 1 WARNING