Last updated on 2025-05-10 16:53:08 CEST.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| fastml | 13 | ||
| genSEIR | 13 | ||
| MVN | 2 | 11 | |
| PubChemR | 13 | ||
| rPDBapi | 1 | 12 |
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: NOTE: 2, OK: 11
Version: 5.9
Check: CRAN incoming feasibility
Result: NOTE
Maintainer: ‘Selcuk Korkmaz <selcukorkmaz@gmail.com>’
Package CITATION file contains call(s) to old-style personList() or
as.personList(). Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry(). Please
use bibentry() instead.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Current CRAN status: OK: 13
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:
> 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
+ )
Warning in search_graphql(graphql_json_query = list(query = json_query)) :
It appears the request failed with: <html><body><h1>503 Service Unavailable</h1>
No server is available to handle this request.
</body></html>
Error in value[[3L]](cond) :
Failed to fetch data from PDB. Error: ERROR: GraphQL query execution failed. Details: Request failed.
Calls: data_fetcher ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Flavor: r-release-linux-x86_64
Version: 2.1.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [125s/432s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(rPDBapi)
>
> test_check("rPDBapi")
[ FAIL 8 | WARN 1046 | SKIP 0 | PASS 57 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_data_fetcher.R:11:3'): data_fetcher returns correct structure ──
Error in `value[[3L]](cond)`: Failed to fetch data from PDB. Error: ERROR: GraphQL query execution failed. Details: Request failed.
Backtrace:
▆
1. └─rPDBapi::data_fetcher(...) at test_data_fetcher.R:11:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Failure ('test_find_results.R:6:3'): find_papers returns correct paper titles ──
length(result) > 0 is not TRUE
`actual`: FALSE
`expected`: TRUE
── Error ('test_find_results.R:7:3'): find_papers returns correct paper titles ──
<subscriptOutOfBoundsError/error/condition>
Error in `result[[1]]`: subscript out of bounds
Backtrace:
▆
1. └─testthat::expect_type(result[[1]], "character") at test_find_results.R:7:3
2. └─testthat::quasi_label(enquo(object), arg = "object")
3. └─rlang::eval_bare(expr, quo_get_env(quo))
── Failure ('test_find_results.R:15:3'): find_results returns correct field information ──
length(result) > 0 is not TRUE
`actual`: FALSE
`expected`: TRUE
── Error ('test_find_results.R:16:3'): find_results returns correct field information ──
<subscriptOutOfBoundsError/error/condition>
Error in `result[[1]]`: subscript out of bounds
Backtrace:
▆
1. └─testthat::expect_type(result[[1]], "list") at test_find_results.R:16:3
2. └─testthat::quasi_label(enquo(object), arg = "object")
3. └─rlang::eval_bare(expr, quo_get_env(quo))
── Error ('test_get_fasta_from_rcsb_entry.R:5:3'): get_fasta_from_rcsb_entry returns correct FASTA sequences ──
Error in `get_fasta_from_rcsb_entry("4HHB")`: Request failed with status code : <html><body><h1>503 Service Unavailable</h1>
No server is available to handle this request.
</body></html>
Backtrace:
▆
1. └─rPDBapi::get_fasta_from_rcsb_entry("4HHB") at test_get_fasta_from_rcsb_entry.R:5:3
── Error ('test_get_fasta_from_rcsb_entry.R:13:3'): get_fasta_from_rcsb_entry returns correct chain sequence ──
Error in `get_fasta_from_rcsb_entry("4HHB", chain_id = "A")`: Request failed with status code : <html><body><h1>503 Service Unavailable</h1>
No server is available to handle this request.
</body></html>
Backtrace:
▆
1. └─rPDBapi::get_fasta_from_rcsb_entry("4HHB", chain_id = "A") at test_get_fasta_from_rcsb_entry.R:13:3
── Error ('test_get_info.R:3:3'): get_info retrieves correct PDB information ───
Error in `value[[3L]](cond)`: API Error: Failed to retrieve data for PDB ID '4HHB'. Error: HTTP Error: Request to https://data.rcsb.org/rest/v1/core/entry/4HHB failed with status: - Server error: (503) Service Unavailable
Backtrace:
▆
1. └─rPDBapi::get_info("4HHB") at test_get_info.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 8 | WARN 1046 | SKIP 0 | PASS 57 ]
Error: Test failures
Execution halted
Flavor: r-release-linux-x86_64