• using R version 4.5.2 Patched (2026-01-31 r89374)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-14 (Debian 14.3.0-10) 14.3.0     GNU Fortran (Debian 14.3.0-10) 14.3.0
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8
• checking for file ‘oncomsm/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘oncomsm’ version ‘0.1.4’
• 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 ‘oncomsm’ can be installed ... OK See the install log for details.
• used C++ compiler: ‘g++-14 (Debian 14.3.0-10) 14.3.0’
• checking C++ specification ... OK
• 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 ... [5s/5s] OK
• checking whether the package can be loaded with stated dependencies ... [4s/5s] OK
• checking whether the package can be unloaded cleanly ... [4s/6s] OK
• checking whether the namespace can be loaded with stated dependencies ... [4s/5s] OK
• checking whether the namespace can be unloaded cleanly ... [5s/6s] OK
• checking loading without being on the library search path ... [8s/10s] 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 ... [21s/27s] OK
• checking Rd files ... [0s/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 line endings in shell scripts ... OK
• checking line endings in C/C++/Fortran sources/headers ... OK
• checking line endings in Makefiles ... OK
• checking compilation flags in Makevars ... OK
• checking for GNU extensions in Makefiles ... INFO GNU make is a SystemRequirements.
• checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
• checking use of PKG_*FLAGS in Makefiles ... OK
• checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
• checking pragmas in C/C++ headers and code ... OK
• checking compilation flags used ... OK
• checking compiled code ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [16s/20s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [111s/151s] OK   Running ‘testthat.R’ [111s/150s]
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [64s/92s] ERROR Error(s) in re-building vignettes:   ... --- re-building ‘avoiding-bias.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘avoiding-bias.Rmd’ --- re-building ‘oncomsm.Rmd’ using rmarkdown Quitting from oncomsm.Rmd:256-272 [unnamed-chunk-2] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `summarize()`: ℹ In argument: `dt = t - lag(t)`. ℹ In group 1: `iter = 1`, `group_id = "A"`, `subject_id = "ID00827488"`. Caused by error: ! `dt` must be size 1, not 3. ℹ To return more or less than 1 row per group, use `reframe()`. --- Backtrace:     ▆  1. ├─... %>% ...  2. ├─dplyr::summarize(., `median transition time` = median(dt), .groups = "drop")  3. ├─dplyr::group_by(., group_id, from, to)  4. ├─dplyr::filter(., to != "stable")  5. ├─dplyr::summarize(...)  6. ├─dplyr:::summarise.grouped_df(., dt = t - lag(t), from = lag(state), to = state, .groups = "drop")  7. │ └─dplyr:::summarise_cols(.data, dplyr_quosures(...), by, "summarise")  8. │ └─base::withCallingHandlers(...)  9. └─dplyr:::dplyr_internal_error(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'oncomsm.Rmd' failed with diagnostics: ℹ In argument: `dt = t - lag(t)`. ℹ In group 1: `iter = 1`, `group_id = "A"`, `subject_id = "ID00827488"`. Caused by error: ! `dt` must be size 1, not 3. ℹ To return more or less than 1 row per group, use `reframe()`. --- failed re-building ‘oncomsm.Rmd’ --- re-building ‘prior-choice.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘prior-choice.Rmd’ SUMMARY: processing the following file failed:   ‘oncomsm.Rmd’ Error: Vignette re-building failed. Execution halted
• checking PDF version of manual ... [5s/6s] OK
• checking HTML version of manual ... [1s/1s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR