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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:LRBaseDbi.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings LRBaseDbi_2.20.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/LRBaseDbi.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘LRBaseDbi/DESCRIPTION’ ... OK
* this is package ‘LRBaseDbi’ version ‘2.20.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://bioconductor.org/packages/3.22/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.22/data/annotation/src/contrib/PACKAGES'
 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 ‘LRBaseDbi’ 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 whether startup messages can be suppressed ... 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 ... 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 ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘LRBaseDbi.Rnw’ using Sweave
LRBase.XXX.eg.db-type packages are deprecated since Bioconductor 3.14. Use AnnotationHub instead. For details, check the vignette of LRBaseDbi
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: ‘generics’

The following objects are masked from ‘package:base’:

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: BiocFileCache
Loading required package: dbplyr

Error: processing vignette 'LRBaseDbi.Rnw' failed with diagnostics:
 chunk 2 
Error in value[[3L]](cond) : failed to connect
  reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [bioconductor.org]:
SSL connection timeout
  Consider rerunning with 'localHub=TRUE'

--- failed re-building ‘LRBaseDbi.Rnw’

SUMMARY: processing the following file failed:
  ‘LRBaseDbi.Rnw’

Error: Vignette re-building failed.
Execution halted

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

Status: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/LRBaseDbi.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL LRBaseDbi
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘LRBaseDbi’ ...
** this is package ‘LRBaseDbi’ version ‘2.20.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (LRBaseDbi)

R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library("testthat")
> 
> # Setting
> options(testthat.use_colours = FALSE)
> 
> test_file("testthat/test_methods.R")

══ Testing test_methods.R ══════════════════════════════════════════════════════

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]

── Error ('test_methods.R:5:1'): (code run outside of `test_that()`) ───────────
Error in `value[[3L]](cond)`: failed to connect
  reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [bioconductor.org]:
SSL connection timeout
  Consider rerunning with 'localHub=TRUE'
Backtrace:
    ▆
 1. └─AnnotationHub::AnnotationHub() at test_methods.R:5:1
 2.   └─AnnotationHub::.Hub(...)
 3.     └─base::tryCatch(...)
 4.       └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 5.         └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 6.           └─value[[3L]](cond)

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
> 
> proc.time()
   user  system elapsed 
  4.736   0.338  15.278