* using log directory ‘/Users/ripley/R/packages/tests-devel/rPDBapi.Rcheck’
* using R Under development (unstable) (2026-07-10 r90234)
* using platform: aarch64-apple-darwin25.5.0
* R was compiled by
    Apple clang version 21.0.0 (clang-2100.1.1.101)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.5.2
* using session charset: UTF-8
* current time: 2026-07-11 10:53:05 UTC
* using option ‘--no-stop-on-test-error’
* checking for file ‘rPDBapi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rPDBapi’ version ‘3.0.1’
* 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 executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘rPDBapi’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... 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 ... OK
* checking Rd files ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [14s/33s] ERROR
Error(s) in re-building vignettes:
--- re-building ‘rPDBapi-structural-bioinformatics.Rmd’ using rmarkdown

Quitting from rPDBapi-structural-bioinformatics.Rmd:1005-1014 [structure-search]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! RCSB search request failed with status : Server error: (500) Internal Server Error
Response content: {
  "status" : 500,
  "message" : "java.net.ConnectException: Connection refused",
  "link" : "https://search.rcsb.org/redoc/index.html"
}
---
Backtrace:
    ▆
 1. └─rPDBapi::perform_search(...)
 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: processing vignette 'rPDBapi-structural-bioinformatics.Rmd' failed with diagnostics:
RCSB search request failed with status : Server error: (500) Internal Server Error
Response content: {
  "status" : 500,
  "message" : "java.net.ConnectException: Connection refused",
  "link" : "https://search.rcsb.org/redoc/index.html"
}
--- failed re-building ‘rPDBapi-structural-bioinformatics.Rmd’

SUMMARY: processing the following file failed:
  ‘rPDBapi-structural-bioinformatics.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* checking HTML version of manual ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 1 ERROR
See
  ‘/Users/ripley/R/packages/tests-devel/rPDBapi.Rcheck/00check.log’
for details.

       60.51 real        31.75 user         6.97 sys