• using R Under development (unstable) (2025-12-21 r89215)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)     GNU Fortran (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)
• running under: Fedora Linux 42 (Workstation Edition)
• using session charset: UTF-8
• using option ‘--no-stop-on-test-error’
• checking for file ‘msSPChelpR/DESCRIPTION’ ... OK
• this is package ‘msSPChelpR’ version ‘0.9.1’
• 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 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 ‘msSPChelpR’ can be installed ... [22s/27s] OK See the install log for details.
• 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 ... OK
• checking whether the package can be loaded with stated dependencies ... OK
• checking whether the package can be unloaded cleanly ... OK
• checking whether the namespace can be loaded with stated dependencies ... OK
• checking whether the namespace can be unloaded cleanly ... OK
• checking loading without being on the library search path ... 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 ... [27s/34s] OK
• checking Rd files ... 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 ... 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 ... [24s/33s] ERROR Running examples in ‘msSPChelpR-Ex.R’ failed The error most likely occurred in: > ### Name: renumber_time_id_tt > ### Title: Renumber the time ID per case (i.e. Tumor sequence) - tidytable > ### version > ### Aliases: renumber_time_id_tt > > ### ** Examples > > > data(us_second_cancer) > us_second_cancer %>% + #only select first 10000 rows so example runs faster + dplyr::slice(1:10000) %>% + msSPChelpR::renumber_time_id_tt(new_time_id_var = "t_tumid", + dattype = "seer", + case_id_var = "fake_id") Error in `[.data.table`(~.df, , `:=`(t_tumid = as.integer(seq_len(.N))), :   attempt access index 16/16 in VECTOR_ELT Calls: %>% ... <Anonymous> -> mutate.tidytable -> eval_tidy -> [ -> [.data.table Execution halted
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [8s/10s] OK   Running ‘testthat.R’
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [24s/34s] ERROR Error(s) in re-building vignettes: --- re-building ‘introduction.Rmd’ using rmarkdown Quitting from introduction.Rmd:236-258 [unnamed-chunk-10] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `[.data.table`: ! attempt access index 11/11 in VECTOR_ELT --- Backtrace:      ▆   1. ├─usdata_wide %>% ...   2. ├─msSPChelpR::sir_byfutime(...)   3. │ └─... %>% tidytable::filter(n > 1)   4. ├─tidytable::filter(., n > 1)   5. ├─tidytable::add_count(...)   6. ├─tidytable:::add_count.tidytable(...)   7. │ ├─tidytable::mutate(.df, `:=`(!!name, n()), .by = c(!!!.by))   8. │ └─tidytable:::mutate.tidytable(.df, `:=`(!!name, n()), .by = c(!!!.by))   9. │ └─rlang::eval_tidy(dt_expr, .df, dt_env)  10. ├─.df[, `:=`(n = .N), by = `<chr>`, keyby = FALSE]  11. └─data.table:::`[.data.table`(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'introduction.Rmd' failed with diagnostics: attempt access index 11/11 in VECTOR_ELT --- failed re-building ‘introduction.Rmd’ SUMMARY: processing the following file failed:   ‘introduction.Rmd’ Error: Vignette re-building failed. Execution halted
• checking PDF version of manual ... [8s/11s] OK
• checking HTML version of manual ... OK
• checking for non-standard things in the check directory ... OK
• checking for detritus in the temp directory ... OK
• DONE

Status: 2 ERRORs