===============================
R CMD BUILD
===============================
* checking for file ‘scGraphVerse/DESCRIPTION’ ... OK
* preparing ‘scGraphVerse’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘case_study.Rmd’ using rmarkdown
trying URL 'https://stringdb-downloads.org/download/protein.aliases.v11.5/9606.protein.aliases.v11.5.txt.gz'
Content type 'application/octet-stream' length 21726816 bytes (20.7 MB)
==================================================
downloaded 20.7 MB
trying URL 'https://stringdb-downloads.org/download/protein.info.v11.5/9606.protein.info.v11.5.txt.gz'
Content type 'application/octet-stream' length 1901833 bytes (1.8 MB)
==================================================
downloaded 1.8 MB
--- finished re-building ‘case_study.Rmd’
--- re-building ‘simulation_study.Rmd’ using rmarkdown
Quitting from simulation_study.Rmd:355-357 [sessioninfo]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `x[["Version"]]`:
! subscript out of bounds
---
Backtrace:
▆
1. └─tools::buildVignettes(dir = ".", tangle = TRUE)
2. ├─base::tryCatch(...)
3. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
6. └─engine$weave(file, quiet = quiet, encoding = enc)
7. └─knitr:::vweave_rmarkdown(...)
8. └─rmarkdown::render(...)
9. └─knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
10. └─knitr:::process_file(text, output)
11. ├─xfun:::handle_error(...)
12. ├─base::withCallingHandlers(...)
13. └─knitr:::process_group(group)
14. └─knitr:::call_block(x)
15. └─knitr:::block_exec(params)
16. └─knitr:::eng_r(options)
17. ├─knitr:::in_input_dir(...)
18. │ └─knitr:::in_dir(input_dir(), expr)
19. └─knitr (local) evaluate(...)
20. └─evaluate::evaluate(...)
21. ├─base::withRestarts(...)
22. │ └─base (local) withRestartList(expr, restarts)
23. │ ├─base (local) withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
24. │ │ └─base (local) doWithOneRestart(return(expr), restart)
25. │ └─base (local) withRestartList(expr, restarts[-nr])
26. │ └─base (local) withOneRestart(expr, restarts[[1L]])
27. │ └─base (local) doWithOneRestart(return(expr), restart)
28. ├─evaluate:::with_handlers(...)
29. │ ├─base::eval(call)
30. │ │ └─base::eval(call)
31. │ └─base::withCallingHandlers(...)
32. └─watcher$print_value(ev$value, ev$visible, envir)
33. ├─base::withVisible(handle_value(handler, value, visible, envir))
34. └─evaluate:::handle_value(handler, value, visible, envir)
35. └─handler$value(value, visible)
36. └─knitr (local) fun(x, options = options)
37. ├─base::withVisible(knit_print(x, ...))
38. ├─knitr::knit_print(x, ...)
39. └─knitr:::knit_print.default(x, ...)
40. └─knitr::normal_print(x)
41. ├─base::print(x)
42. └─utils:::print.sessionInfo(x)
43. ├─base::print(mkLabel(x, "loadedOnly"), quote = FALSE, ...)
44. └─utils (local) mkLabel(x, "loadedOnly")
45. └─base::sapply(L[[n]], function(x) x[["Version"]])
46. └─base::lapply(X = X, FUN = FUN, ...)
47. └─utils (local) FUN(X[[i]], ...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'simulation_study.Rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building ‘simulation_study.Rmd’
SUMMARY: processing the following file failed:
‘simulation_study.Rmd’
Error: Vignette re-building failed.
Execution halted