Last updated on 2025-09-11 21:51:04 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.1.1 | 6.16 | 88.13 | 94.29 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.1.1 | 4.11 | 65.58 | 69.69 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2.1.1 | 143.25 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2.1.1 | 130.00 | OK | |||
| r-devel-windows-x86_64 | 2.1.1 | 8.00 | 255.00 | 263.00 | OK | |
| r-patched-linux-x86_64 | 2.1.1 | 5.54 | 81.03 | 86.57 | OK | |
| r-release-linux-x86_64 | 2.1.1 | 5.89 | 80.54 | 86.43 | OK | |
| r-release-macos-arm64 | 2.1.1 | 220.00 | OK | |||
| r-release-macos-x86_64 | 2.1.1 | 248.00 | OK | |||
| r-release-windows-x86_64 | 2.1.1 | 8.00 | 214.00 | 222.00 | OK | |
| r-oldrel-macos-arm64 | 2.1.1 | 198.00 | OK | |||
| r-oldrel-macos-x86_64 | 2.1.1 | 219.00 | OK | |||
| r-oldrel-windows-x86_64 | 2.1.1 | 10.00 | 269.00 | 279.00 | ERROR |
Version: 2.1.1
Check: examples
Result: ERROR
Running examples in 'rPDBapi-Ex.R' failed
The error most likely occurred in:
> ### 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 in value[[3L]](cond) :
Failed to retrieve data from the RCSB PDB. Network error: Timeout was reached [www.rcsb.org]:
Connection timed out after 10008 milliseconds
Calls: get_fasta_from_rcsb_entry ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Flavor: r-oldrel-windows-x86_64
Version: 2.1.1
Check: tests
Result: ERROR
Running 'testthat.R' [175s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(rPDBapi)
>
> test_check("rPDBapi")
[ FAIL 3 | WARN 0 | SKIP 0 | PASS 65 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_get_fasta_from_rcsb_entry.R:5:3'): get_fasta_from_rcsb_entry returns correct FASTA sequences ──
Error in `value[[3L]](cond)`: Failed to retrieve data from the RCSB PDB. Network error: Timeout was reached [www.rcsb.org]:
Connection timed out after 10012 milliseconds
Backtrace:
▆
1. └─rPDBapi::get_fasta_from_rcsb_entry("4HHB") at test_get_fasta_from_rcsb_entry.R:5:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test_get_fasta_from_rcsb_entry.R:13:3'): get_fasta_from_rcsb_entry returns correct chain sequence ──
Error in `value[[3L]](cond)`: Failed to retrieve data from the RCSB PDB. Network error: Timeout was reached [www.rcsb.org]:
Connection timed out after 10014 milliseconds
Backtrace:
▆
1. └─rPDBapi::get_fasta_from_rcsb_entry("4HHB", chain_id = "A") at test_get_fasta_from_rcsb_entry.R:13:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test_get_pdb_file.R:3:3'): get_pdb_file downloads and parses the PDB file correctly ──
Error in `value[[3L]](cond)`: API Error: Failed to retrieve data for PDB ID '4HHB'. Error: HTTP Error: Request to https://files.rcsb.org/download/4HHB.pdb.gz failed with status: - Server error: (503) Service Unavailable
Backtrace:
▆
1. └─rPDBapi::get_pdb_file("4HHB", filetype = "pdb", save = FALSE) at test_get_pdb_file.R:3:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
[ FAIL 3 | WARN 0 | SKIP 0 | PASS 65 ]
Error: Test failures
Execution halted
Flavor: r-oldrel-windows-x86_64