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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:animalcules.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings animalcules_1.21.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/animalcules.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘animalcules/DESCRIPTION’ ... OK
* this is package ‘animalcules’ version ‘1.21.0’
* 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 ‘animalcules’ 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 ‘animalcules-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: find_taxon_mat
> ### Title: Find the Taxonomy Information Matrix
> ### Aliases: find_taxon_mat
> 
> ### ** Examples
> 
> ids <- c("ti|54005", "ti|73001", "ti|573", "ti|228277", "ti|53458")
> tids <- c("54005", "73001", "573", "228277", "53458")
> taxonLevels <- find_taxonomy(tids)
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: [eutils.ncbi.nlm.nih.gov] Resolving timed out after 10000 milliseconds
Calls: find_taxonomy ... request_fetch -> request_fetch.write_memory -> <Anonymous>
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:
       ▆
    1. └─animalcules::find_taxonomy(1200) at test-examples.R:286:3
    2.   └─animalcules::find_taxonomy_300(tids)
    3.     └─rentrez::entrez_fetch(db = "taxonomy", id = tids, rettype = "xml")
    4.       ├─base::do.call(make_entrez_query, args)
    5.       └─rentrez (local) `<fn>`(...)
    6.         └─httr::GET(uri, query = args, config = config)
    7.           └─httr:::request_perform(req, hu$handle$handle)
    8.             ├─httr:::request_fetch(req$output, req$url, handle)
    9.             └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   10.               └─curl::curl_fetch_memory(url, handle = handle)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 37 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/animalcules.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL animalcules
###
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* installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’
* installing *source* package ‘animalcules’ ...
** 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 (animalcules)

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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)
> library(animalcules)
> 
> test_check("animalcules")
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 37 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-examples.R:286:3'): find_taxonomy() is working ─────────────────
Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached: [eutils.ncbi.nlm.nih.gov] Resolving timed out after 10000 milliseconds
Backtrace:
     ▆
  1. └─animalcules::find_taxonomy(1200) at test-examples.R:286:3
  2.   └─animalcules::find_taxonomy_300(tids)
  3.     └─rentrez::entrez_fetch(db = "taxonomy", id = tids, rettype = "xml")
  4.       ├─base::do.call(make_entrez_query, args)
  5.       └─rentrez (local) `<fn>`(...)
  6.         └─httr::GET(uri, query = args, config = config)
  7.           └─httr:::request_perform(req, hu$handle$handle)
  8.             ├─httr:::request_fetch(req$output, req$url, handle)
  9.             └─httr:::request_fetch.write_memory(req$output, req$url, handle)
 10.               └─curl::curl_fetch_memory(url, handle = handle)

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 37 ]
Error: Test failures
Execution halted