Last updated on 2026-08-16 05:50:26 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 3.0.1 | 7.13 | 276.70 | 283.83 | OK | |
| r-devel-linux-x86_64-debian-gcc | 3.0.1 | 5.11 | 161.28 | 166.39 | OK | |
| r-devel-linux-x86_64-fedora-clang | 3.0.1 | 177.23 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 3.0.1 | 173.77 | OK | |||
| r-devel-windows-x86_64 | 3.0.1 | 11.00 | 325.00 | 336.00 | ERROR | |
| r-patched-linux-x86_64 | 3.0.1 | 8.08 | 261.30 | 269.38 | OK | |
| r-release-linux-x86_64 | 3.0.1 | 6.05 | 262.11 | 268.16 | ERROR | |
| 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 | 330.00 | 340.00 | 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 | 13.00 | 411.00 | 424.00 | OK |
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:1471-1488 [fetch-contracts]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! Failed to fetch data from PDB. Error: ERROR: GraphQL query execution failed. Details: Request failed.
---
Backtrace:
▆
1. └─rPDBapi::data_fetcher(...)
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
6. └─rPDBapi:::rpdbapi_rethrow(...)
7. └─rPDBapi:::rpdbapi_abort(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'rPDBapi-structural-bioinformatics.Rmd' failed with diagnostics:
Failed to fetch data from PDB. Error: ERROR: GraphQL query execution failed. Details: Request failed.
--- 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-windows-x86_64
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: get_fasta_from_rcsb_entry
> ### Title: Retrieve FASTA Sequence from PDB Entry or Specific Chain
> ### Aliases: get_fasta_from_rcsb_entry
>
> ### ** Examples
>
> # Example 1: Retrieve all FASTA sequences for the entry 4HHB
> all_sequences <- get_fasta_from_rcsb_entry("4HHB", verbosity = TRUE)
Querying RCSB for the '4HHB' FASTA file.
Error: Failed to retrieve data from the RCSB PDB. Network error: Timeout was reached [www.rcsb.org]:
Connection timed out after 10001 milliseconds
Execution halted
Flavor: r-release-linux-x86_64