CRAN Package Check Results for Package r3dmol

Last updated on 2025-08-22 21:48:36 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.1.2 3.68 65.95 69.63 OK
r-devel-linux-x86_64-debian-gcc 0.1.2 2.99 44.19 47.18 ERROR
r-devel-linux-x86_64-fedora-clang 0.1.2 104.72 OK
r-devel-linux-x86_64-fedora-gcc 0.1.2 114.66 OK
r-devel-windows-x86_64 0.1.2 9.00 106.00 115.00 OK
r-patched-linux-x86_64 0.1.2 5.77 60.79 66.56 OK
r-release-linux-x86_64 0.1.2 4.28 61.67 65.95 OK
r-release-macos-arm64 0.1.2 47.00 OK
r-release-macos-x86_64 0.1.2 82.00 OK
r-release-windows-x86_64 0.1.2 10.00 110.00 120.00 OK
r-oldrel-macos-arm64 0.1.2 53.00 NOTE
r-oldrel-macos-x86_64 0.1.2 79.00 NOTE
r-oldrel-windows-x86_64 0.1.2 12.00 129.00 141.00 NOTE

Check Details

Version: 0.1.2
Check: examples
Result: ERROR Running examples in ‘r3dmol-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### 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-devel-linux-x86_64-debian-gcc

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-devel-linux-x86_64-debian-gcc

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