Last updated on 2025-09-13 00:51:28 CEST.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| pagemap | 13 | ||
| r3dmol | 1 | 2 | 10 |
Current CRAN status: OK: 13
Current CRAN status: ERROR: 1, NOTE: 2, OK: 10
Version: 0.1.2
Check: installed package size
Result: NOTE
installed size is 11.5Mb
sub-directories of 1Mb or more:
doc 9.9Mb
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Version: 0.1.2
Check: examples
Result: ERROR
Running examples in 'r3dmol-Ex.R' failed
The error most likely occurred in:
> ### Name: m_add_sphere
> ### Title: Add Sphere Shape
> ### Aliases: m_add_sphere
>
> ### ** Examples
>
> r3dmol() %>%
+ m_add_model(data = m_fetch_pdb("1bna")) %>%
+ m_add_sphere(
+ center = m_sel(resi = 1),
+ spec = m_shape_spec(color = "green", wireframe = TRUE)
+ ) %>%
+ m_zoom_to(sel = m_sel(resi = 1))
Warning in file(con, "r") :
cannot open URL 'https://files.rcsb.org/download/1bna.pdb': HTTP status was '503 Service Unavailable'
Error in file(con, "r") :
cannot open the connection to 'https://files.rcsb.org/download/1bna.pdb'
Calls: %>% ... as.list.environment -> m_add_model -> m_fetch_pdb -> readLines -> file
Execution halted
Flavor: r-oldrel-windows-x86_64
Version: 0.1.2
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building 'r3dmol.Rmd' using rmarkdown
--- finished re-building 'r3dmol.Rmd'
--- re-building 'style-functions.Rmd' using rmarkdown
Quitting from style-functions.Rmd:171-177 [unnamed-chunk-6]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `file()`:
! cannot open the connection to 'https://files.rcsb.org/download/1bna.pdb'
---
Backtrace:
▆
1. ├─... %>% m_zoom_to()
2. ├─r3dmol::m_zoom_to(.)
3. │ └─r3dmol:::callJS()
4. │ ├─base::Filter(function(x) !is.symbol(x), as.list(parent.frame(1)))
5. │ │ ├─base::unlist(lapply(x, f))
6. │ │ └─base::lapply(x, f)
7. │ ├─base::as.list(parent.frame(1))
8. │ └─base::as.list.environment(parent.frame(1))
9. ├─r3dmol::m_set_style(., style = m_style_cartoon())
10. │ └─r3dmol:::callJS()
11. │ ├─base::Filter(function(x) !is.symbol(x), as.list(parent.frame(1)))
12. │ │ ├─base::unlist(lapply(x, f))
13. │ │ └─base::lapply(x, f)
14. │ ├─base::as.list(parent.frame(1))
15. │ └─base::as.list.environment(parent.frame(1))
16. ├─r3dmol::m_add_model(., data = m_fetch_pdb("1bna", save.pdb = FALSE))
17. └─r3dmol::m_fetch_pdb("1bna", save.pdb = FALSE)
18. └─base::readLines(bio3d::get.pdb(pdb, URLonly = TRUE))
19. └─base::file(con, "r")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'style-functions.Rmd' failed with diagnostics:
cannot open the connection to 'https://files.rcsb.org/download/1bna.pdb'
--- failed re-building 'style-functions.Rmd'
SUMMARY: processing the following file failed:
'style-functions.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-oldrel-windows-x86_64