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### Running command:
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###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:celldex.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings celldex_1.14.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.19-data-experiment/meat/celldex.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘celldex/DESCRIPTION’ ... OK
* this is package ‘celldex’ version ‘1.14.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘celldex’ 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 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘celldex-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: listReferences
> ### Title: List available references
> ### Aliases: listReferences listVersions fetchLatestVersion
> 
> ### ** Examples
> 
> listReferences()
Error in `req_perform()`:
! Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached: [gypsum.artifactdb.com] SSL connection timeout
Backtrace:
    ▆
 1. └─celldex::listReferences()
 2.   └─gypsum::listAssets("celldex")
 3.     └─gypsum:::list_for_prefix(paste0(project, "/"), url = url)
 4.       └─httr2::req_perform(req)
 5.         └─base::tryCatch(...)
 6.           └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 7.             └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 8.               └─value[[3L]](cond)
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. └─celldex::DatabaseImmuneCellExpressionData(ensembl = TRUE)
    7.   └─celldex:::.convert_to_ensembl(se, "Hs", ensembl)
    8.     └─AnnotationHub::AnnotationHub()
    9.       └─AnnotationHub::.Hub(...)
   10.         └─base::tryCatch(...)
   11.           └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   12.             └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   13.               └─value[[3L]](cond)
  
  [ FAIL 2 | WARN 10 | SKIP 0 | PASS 30 ]
  Error: Test failures
  In addition: Warning message:
  call dbDisconnect() when finished working with a connection 
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘userguide.Rmd’ using rmarkdown

Quitting from lines 59-61 [unnamed-chunk-2] (userguide.Rmd)
Error: processing vignette 'userguide.Rmd' failed with diagnostics:
Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_disk()`:
! Timeout was reached: [github.com] SSL connection timeout
--- failed re-building ‘userguide.Rmd’

SUMMARY: processing the following file failed:
  ‘userguide.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 3 ERRORs
See
  ‘/home/biocbuild/bbs-3.19-data-experiment/meat/celldex.Rcheck/00check.log’
for details.