Last updated on 2026-06-14 12:49:50 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 3.0.1 | 6.68 | 275.14 | 281.82 | OK | |
| r-devel-linux-x86_64-debian-gcc | 3.0.1 | 4.84 | 49.96 | 54.80 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 3.0.1 | 12.00 | 432.61 | 444.61 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 3.0.1 | 14.00 | 527.28 | 541.28 | OK | |
| r-devel-windows-x86_64 | 3.0.1 | 11.00 | 403.00 | 414.00 | OK | |
| r-patched-linux-x86_64 | 3.0.1 | 7.93 | 266.12 | 274.05 | OK | |
| r-release-linux-x86_64 | 3.0.1 | 6.14 | 264.10 | 270.24 | OK | |
| r-release-macos-arm64 | 3.0.1 | 2.00 | 109.00 | 111.00 | OK | |
| r-release-macos-x86_64 | 3.0.1 | 5.00 | 310.00 | 315.00 | OK | |
| r-release-windows-x86_64 | 3.0.1 | 10.00 | 299.00 | 309.00 | OK | |
| r-oldrel-macos-arm64 | 3.0.1 | 2.00 | 102.00 | 104.00 | OK | |
| r-oldrel-macos-x86_64 | 3.0.1 | 5.00 | 279.00 | 284.00 | OK | |
| r-oldrel-windows-x86_64 | 3.0.1 | 12.00 | 395.00 | 407.00 | OK |
Version: 3.0.1
Check: examples
Result: ERROR
Running examples in ‘rPDBapi-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: data_fetcher
> ### Title: Fetch RCSB PDB Data Based on Specified Criteria
> ### Aliases: data_fetcher
>
> ### ** Examples
>
> # Example 1: Fetching basic entry information
> properties <- list(cell = c("length_a", "length_b", "length_c"), exptl = c("method"))
> data_fetcher(
+ id = c("4HHB"),
+ data_type = "ENTRY",
+ properties = properties,
+ return_as_dataframe = TRUE
+ )
Error: Failed to fetch data from PDB. Error: ERROR: GraphQL query execution failed. Details: Timeout was reached [data.rcsb.org]:
Connection timed out after 10002 milliseconds
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 3.0.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘rPDBapi-structural-bioinformatics.Rmd’ using rmarkdown
Quitting from rPDBapi-structural-bioinformatics.Rmd:237-243 [simple-search]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! All retrieval attempts failed after 1 tries. Please check the search term, query type, and your network connection.
---
Backtrace:
▆
1. └─rPDBapi::query_search("protein kinase")
2. └─rPDBapi:::rpdbapi_abort(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'rPDBapi-structural-bioinformatics.Rmd' failed with diagnostics:
All retrieval attempts failed after 1 tries. Please check the search term, query type, and your network connection.
--- failed re-building ‘rPDBapi-structural-bioinformatics.Rmd’
SUMMARY: processing the following file failed:
‘rPDBapi-structural-bioinformatics.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc