Last updated on 2025-09-13 00:51:27 CEST.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| fastml | 13 | ||
| genSEIR | 13 | ||
| MVN | 13 | ||
| PubChemR | 3 | 10 | |
| rPDBapi | 1 | 12 |
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: NOTE: 3, OK: 10
Version: 2.1.5
Check: installed package size
Result: NOTE
installed size is 5.0Mb
sub-directories of 1Mb or more:
doc 4.7Mb
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Current CRAN status: ERROR: 1, OK: 12
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