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### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:fenr.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings fenr_1.0.5.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/fenr.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* 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 ‘fenr/DESCRIPTION’ ... OK
* this is package ‘fenr’ version ‘1.0.5’
* 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 ‘fenr’ 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 R 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘fenr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: enrichment_interactive
> ### Title: Small Shiny app serving as example for fast enrichment
> ### Aliases: enrichment_interactive
> 
> ### ** Examples
> 
> data(yeast_de)
> term_data <- fetch_terms_for_example(yeast_de)
Fetching GO data

Fetching Reactome data

Error in `httr2::req_perform()`:
! Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached: [reactome.org] SSL connection timeout
Backtrace:
     ▆
  1. └─fenr::fetch_terms_for_example(yeast_de)
  2.   └─fenr::fetch_reactome("Saccharomyces cerevisiae", on_error = "warn")
  3.     └─fenr:::match_species(...)
  4.       └─fenr:::assert_species(species, fetch_fun, on_error)
  5.         └─fenr (local) f(on_error = on_error)
  6.           └─fenr:::api_query(get_reactome_url(), "data/species/main")
  7.             └─httr2::req_perform(httr2::req_error(req, is_error = ~FALSE))
  8.               └─base::tryCatch(...)
  9.                 └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 10.                   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 11.                     └─value[[3L]](cond)
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘fenr.Rmd’ using ‘UTF-8’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/fenr.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL fenr
###
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* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
* installing *source* package ‘fenr’ ...
** using staged installation
** R
** data
** 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 (fenr)

R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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)
> library(fenr)
> 
> test_check("fenr")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 312 ]
> 
> proc.time()
   user  system elapsed 
 47.523   2.235  92.464