Last updated on 2026-02-07 11:49:44 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.1.2 | 5.49 | 92.25 | 97.74 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.1.2 | 3.94 | 41.65 | 45.59 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 2.1.2 | 11.00 | 136.81 | 147.81 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 2.1.2 | 10.00 | 134.43 | 144.43 | OK | |
| r-devel-windows-x86_64 | 2.1.2 | 9.00 | 222.00 | 231.00 | OK | |
| r-patched-linux-x86_64 | 2.1.2 | 6.26 | 81.10 | 87.36 | OK | |
| r-release-linux-x86_64 | 2.1.2 | 5.97 | 80.34 | 86.31 | OK | |
| r-release-macos-arm64 | 2.1.2 | OK | ||||
| r-release-macos-x86_64 | 2.1.2 | 5.00 | 283.00 | 288.00 | OK | |
| r-release-windows-x86_64 | 2.1.2 | 8.00 | 220.00 | 228.00 | OK | |
| r-oldrel-macos-arm64 | 2.1.2 | OK | ||||
| r-oldrel-macos-x86_64 | 2.1.2 | 5.00 | 331.00 | 336.00 | OK | |
| r-oldrel-windows-x86_64 | 2.1.2 | 10.00 | 244.00 | 254.00 | OK |
Version: 2.1.2
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 in value[[3L]](cond) :
Failed to fetch data from PDB. Error: ERROR: GraphQL query execution failed. Details: Timeout was reached [data.rcsb.org]:
Connection timed out after 10000 milliseconds
Calls: data_fetcher ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 2.1.2
Check: tests
Result: ERROR
Running ‘testthat.R’ [0m/11m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(rPDBapi)
>
> test_check("rPDBapi")
Saving _problems/test_find_results-3.R
Saving _problems/test_find_results-12.R
[ FAIL 2 | WARN 2 | SKIP 0 | PASS 66 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_find_results.R:3:3'): find_papers returns correct paper titles ──
Error in `value[[3L]](cond)`: Failed to fetch search results for term 'ribosome'. Error: All retrieval attempts failed after 1 tries. Please check the search term, query type, and your network connection.
Backtrace:
▆
1. └─rPDBapi::find_papers("ribosome", max_results = 2) at test_find_results.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)
── Error ('test_find_results.R:12:3'): find_results returns correct field information ──
Error in `value[[3L]](cond)`: Failed to fetch search results for term 'crispr'. Error: All retrieval attempts failed after 1 tries. Please check the search term, query type, and your network connection.
Backtrace:
▆
1. └─rPDBapi::find_results("crispr", field = "citation") at test_find_results.R:12:3
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 2 | WARN 2 | SKIP 0 | PASS 66 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc