- using R version 4.4.0 (2024-04-24 ucrt)
- using platform: x86_64-w64-mingw32
- R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
- running under: Windows Server 2022 x64 (build 20348)
- using session charset: UTF-8
- checking for file 'rPDBapi/DESCRIPTION' ... OK
- checking extension type ... Package
- this is package 'rPDBapi' version '1.1'
- package encoding: UTF-8
- checking package namespace information ... OK
- checking package dependencies ... OK
- checking if this is a source package ... OK
- checking if there is a namespace ... OK
- checking for hidden files and directories ... OK
- checking for portable file names ... OK
- checking whether package 'rPDBapi' can be installed ... OK
See the install log for details.
- checking installed package size ... OK
- checking package directory ... OK
- checking DESCRIPTION meta-information ... OK
- checking top-level files ... OK
- checking for left-over files ... OK
- checking index information ... OK
- checking package subdirectories ... OK
- checking code files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- checking whether the package can be loaded ... [1s] OK
- checking whether the package can be loaded with stated dependencies ... [1s] OK
- checking whether the package can be unloaded cleanly ... [1s] OK
- checking whether the namespace can be loaded with stated dependencies ... [1s] OK
- checking whether the namespace can be unloaded cleanly ... [1s] OK
- checking loading without being on the library search path ... [1s] OK
- checking use of S3 registration ... OK
- checking dependencies in R code ... OK
- checking S3 generic/method consistency ... OK
- checking replacement functions ... OK
- checking foreign function calls ... OK
- checking R code for possible problems ... [4s] OK
- checking Rd files ... [1s] OK
- checking Rd metadata ... OK
- checking Rd cross-references ... OK
- checking for missing documentation entries ... OK
- checking for code/documentation mismatches ... OK
- checking Rd \usage sections ... OK
- checking Rd contents ... OK
- checking for unstated dependencies in examples ... OK
- checking examples ... [6s] ERROR
Running examples in 'rPDBapi-Ex.R' failed
The error most likely occurred in:
> ### Name: perform_search
> ### Title: Perform a Search in the RCSB PDB
> ### Aliases: perform_search
>
> ### ** Examples
>
> search_operator = InOperator(value=c("Mus musculus", "Homo sapiens"),
+ attribute="rcsb_entity_source_organism.taxonomy_lineage.name")
> return_type = "NON_POLYMER_ENTITY"
> results = perform_search(search_operator, return_type)
Querying RCSB Search with the following parameters:
{
"query": {
"type": "terminal",
"service": "text",
"parameters": {
"attribute": "rcsb_entity_source_organism.taxonomy_lineage.name",
"operator": "in",
"value": ["Mus musculus", "Homo sapiens"]
}
},
"request_options": {
"return_all_hits": true
},
"return_type": "non_polymer_entity"
}
Error in perform_search_with_graph(query_object = search_operator, return_type = return_type, :
Request failed with:{"timestamp":"2024-05-14T13:22:13.437+00:00","status":415,"error":"Unsupported Media Type","path":"/rcsbsearch/v2/query"}
Calls: perform_search -> perform_search_with_graph
Execution halted
- checking PDF version of manual ... [21s] OK
- checking HTML version of manual ... [5s] OK
- DONE
Status: 1 ERROR