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### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:bugphyzz.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings bugphyzz_1.5.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-data-experiment/meat/bugphyzz.Rcheck’
* using R Under development (unstable) (2026-01-15 r89304)
* 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 ‘bugphyzz/DESCRIPTION’ ... OK
* this is package ‘bugphyzz’ version ‘1.5.0’
* 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 ‘bugphyzz’ 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 R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
physiologies       55.195  2.125 122.544
getTaxonSignatures 16.468  0.945  18.317
makeSignatures     12.564  0.487  13.942
importBugphyzz     12.167  0.595  13.524
* 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. ├─base::suppressWarnings(physiologies()) at test-physiologies.R:3:1
    2. │ └─base::withCallingHandlers(...)
    3. └─bugphyzz::physiologies()
    4.   └─bugphyzz:::.importSpreadsheets(keyword = keyword)
    5.     └─base::lapply(...)
    6.       └─bugphyzz (local) FUN(X[[i]], ...)
    7.         ├─dplyr::distinct(utils::read.csv(url))
    8.         └─utils::read.csv(url)
    9.           └─utils::read.table(...)
   10.             └─base::file(file, "rt")
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 23 ]
  Error:
  ! Test failures.
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.23-data-experiment/meat/bugphyzz.Rcheck/00check.log’
for details.

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###
### Running command:
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###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL bugphyzz
###
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘bugphyzz’ ...
** this is package ‘bugphyzz’ version ‘1.5.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (bugphyzz)

R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"
Copyright (C) 2026 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)
> library(bugphyzz)
> 
> test_check("bugphyzz")
Using data downloaded on 2026-01-15 17:07:59.
Importing binary data...
Downloading, bugphyzz_binary.csv.

Using data downloaded on 2026-01-20 17:08:11.
Importing multistate data...
Replacing previous version downloaded on 2026-01-15 17:07:17.

Using data downloaded on 2026-01-20 17:08:15.
Importing numeric data...
Replacing previous version downloaded on 2026-01-15 17:07:31.

Using data downloaded on 2026-01-20 17:08:26.
Importing binary data...
Replacing previous version downloaded on 2026-01-20 17:08:11.

Using data downloaded on 2026-01-20 17:08:31.
Importing multistate data...
Replacing previous version downloaded on 2026-01-20 17:08:15.

Using data downloaded on 2026-01-20 17:08:35.
Importing numeric data...
Replacing previous version downloaded on 2026-01-20 17:08:26.

Using data downloaded on 2026-01-20 17:08:48.
Saving _problems/test-importBugphyzz-193.R
Loading required package: stats4
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


Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Using data downloaded on 2026-01-15 17:07:59.
Using data downloaded on 2026-01-15 17:07:59.
All physiologies will be imported.
Saving _problems/test-physiologies-3.R
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 23 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-importBugphyzz.R:193:5'): importBugphyzz works with Zenodo DOI ──
<httr2_http_504/httr2_http/httr2_error/rlang_error/rlang_error/error/condition>
Error in `httr2::req_perform(req)`: HTTP 504 Gateway Timeout.
Backtrace:
     ▆
  1. └─bugphyzz::importBugphyzz(...) at test-importBugphyzz.R:193:5
  2.   └─bugphyzz:::.downloadResource(version, forceDownload)
  3.     └─bugphyzz:::.downloadZ(suffix, forceDownload)
  4.       └─httr2::req_perform(req)
  5.         └─httr2:::handle_resp(req, resp, error_call = error_call)
  6.           └─httr2:::resp_failure_cnd(req, resp, error_call = error_call)
  7.             ├─rlang::catch_cnd(...)
  8.             │ ├─rlang::eval_bare(...)
  9.             │ ├─base::tryCatch(...)
 10.             │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 11.             │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 12.             │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 13.             │ └─base::force(expr)
 14.             └─rlang::abort(...)
── Error ('test-physiologies.R:3:1'): (code run outside of `test_that()`) ──────
Error in `file(file, "rt")`: cannot open the connection to 'https://docs.google.com/spreadsheets/d/e/2PACX-1vQkcQ7CJ0LjgE0928maxcVEiqq7QHl6vuosL7qdWaCMVuqHCDwsPJA7yNSeXm9FIip-mDRaU6pMk4Ww/pub?output=csv'
Backtrace:
     ▆
  1. ├─base::suppressWarnings(physiologies()) at test-physiologies.R:3:1
  2. │ └─base::withCallingHandlers(...)
  3. └─bugphyzz::physiologies()
  4.   └─bugphyzz:::.importSpreadsheets(keyword = keyword)
  5.     └─base::lapply(...)
  6.       └─bugphyzz (local) FUN(X[[i]], ...)
  7.         ├─dplyr::distinct(utils::read.csv(url))
  8.         └─utils::read.csv(url)
  9.           └─utils::read.table(...)
 10.             └─base::file(file, "rt")

[ FAIL 2 | WARN 0 | SKIP 0 | PASS 23 ]
Error:
! Test failures.
Execution halted