- using R Under development (unstable) (2025-12-18 r89199)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
gcc-15 (Debian 15.2.0-11) 15.2.0
GNU Fortran (Debian 15.2.0-11) 15.2.0
- running under: Debian GNU/Linux forky/sid
- using session charset: UTF-8
- checking for file ‘spNetwork/DESCRIPTION’ ... OK
- checking extension type ... Package
- this is package ‘spNetwork’ version ‘0.4.4.7’
- 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 ‘spNetwork’ can be installed ... OK
See the install log for details.
- used C++ compiler: ‘g++-15 (Debian 15.2.0-11) 15.2.0’
- 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 ... [2s/3s] OK
- checking whether the package can be loaded with stated dependencies ... [2s/2s] OK
- checking whether the package can be unloaded cleanly ... [2s/2s] OK
- checking whether the namespace can be loaded with stated dependencies ... [2s/3s] OK
- checking whether the namespace can be unloaded cleanly ... [2s/2s] OK
- checking loading without being on the library search path ... [2s/2s] OK
- checking whether startup messages can be suppressed ... [2s/3s] 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 ... [23s/29s] OK
- checking Rd files ... [3s/3s] 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 ... [1s/1s] OK
- checking LazyData ... OK
- checking data for ASCII and uncompressed saves ... 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 ... OK
- checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
- checking use of PKG_*FLAGS in Makefiles ... OK
- checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
- checking pragmas in C/C++ headers and code ... OK
- checking compilation flags used ... OK
- checking compiled code ... NOTE
File ‘spNetwork/libs/spNetwork.so’:
Found non-API call to R: ‘ATTRIB’
Compiled code should not call non-API entry points in R.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
- checking installed files from ‘inst/doc’ ... OK
- checking files in ‘vignettes’ ... OK
- checking examples ... [6s/7s] OK
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [34s/38s] OK
Running ‘testthat.R’ [34s/38s]
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [51s/68s] ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘KNetworkFunctions.Rmd’ using rmarkdown
Quitting from KNetworkFunctions.Rmd:63-77 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 4/4 in VECTOR_ELT
---
Backtrace:
▆
1. └─tools:::.buildOneVignette(...)
2. ├─base::tryCatch(...)
3. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
6. └─engine$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. └─tmap:::knit_print.tmap(x, ...)
40. └─tmap:::print.tmap(x, knit = TRUE, options = options, ...)
41. └─tmap:::step4_plot(...)
42. ├─...[]
43. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'KNetworkFunctions.Rmd' failed with diagnostics:
attempt access index 4/4 in VECTOR_ELT
--- failed re-building ‘KNetworkFunctions.Rmd’
--- re-building ‘NKDE.Rmd’ using rmarkdown
Quitting from NKDE.Rmd:313-331 [unnamed-chunk-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 4/4 in VECTOR_ELT
---
Backtrace:
▆
1. └─tools:::.buildOneVignette(...)
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$value(value, visible)
36. └─knitr (local) fun(x, options = options)
37. ├─base::withVisible(knit_print(x, ...))
38. ├─knitr::knit_print(x, ...)
39. └─tmap:::knit_print.tmap(x, ...)
40. └─tmap:::print.tmap(x, knit = TRUE, options = options, ...)
41. └─tmap:::step4_plot(...)
42. ├─...[]
43. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'NKDE.Rmd' failed with diagnostics:
attempt access index 4/4 in VECTOR_ELT
--- failed re-building ‘NKDE.Rmd’
--- re-building ‘NetworkBuilding.Rmd’ using rmarkdown
Quitting from NetworkBuilding.Rmd:36-51 [unnamed-chunk-1]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 4/4 in VECTOR_ELT
---
Backtrace:
▆
1. └─tools:::.buildOneVignette(...)
2. ├─base::tryCatch(...)
3. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
6. └─engine$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. └─tmap:::knit_print.tmap(x, ...)
40. └─tmap:::print.tmap(x, knit = TRUE, options = options, ...)
41. └─tmap:::step4_plot(...)
42. ├─...[]
43. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'NetworkBuilding.Rmd' failed with diagnostics:
attempt access index 4/4 in VECTOR_ELT
--- failed re-building ‘NetworkBuilding.Rmd’
--- re-building ‘SpatialWeightMatrices.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘SpatialWeightMatrices.Rmd’
--- re-building ‘TNKDE.Rmd’ using rmarkdown
Quitting from TNKDE.Rmd:155-164 [unnamed-chunk-6]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 4/4 in VECTOR_ELT
---
Backtrace:
▆
1. └─tools:::.buildOneVignette(...)
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. └─tmap:::knit_print.tmap(x, ...)
40. └─tmap:::print.tmap(x, knit = TRUE, options = options, ...)
41. └─tmap:::step4_plot(...)
42. ├─...[]
43. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'TNKDE.Rmd' failed with diagnostics:
attempt access index 4/4 in VECTOR_ELT
--- failed re-building ‘TNKDE.Rmd’
SUMMARY: processing the following files failed:
‘KNetworkFunctions.Rmd’ ‘NKDE.Rmd’ ‘NetworkBuilding.Rmd’ ‘TNKDE.Rmd’
Error: Vignette re-building failed.
Execution halted
- checking PDF version of manual ... [8s/11s] OK
- checking HTML version of manual ... [8s/14s] OK
- checking for non-standard things in the check directory ... OK
- DONE
Status: 1 ERROR, 1 NOTE