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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:OmicsMLRepoR.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings OmicsMLRepoR_1.5.5.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/OmicsMLRepoR.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-04-23 06:51:55 UTC
* checking for file ‘OmicsMLRepoR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmicsMLRepoR’ version ‘1.5.5’
* 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 ‘OmicsMLRepoR’ 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 ... NOTE
.getAllTargetForms: no visible binding for global variable ‘.’
.getOntos: no visible binding for global variable ‘.’
availableTerms: no visible binding for global variable ‘.’
ontoTreePlot: no visible binding for global variable ‘iri’
ontoTreePlot: no visible binding for global variable ‘id’
ontoTreePlot: no visible binding for global variable ‘text’
ontoTreePlot: no visible binding for global variable ‘parent’
ontoTreePlot: no visible binding for global variable ‘from’
ontoTreePlot: no visible binding for global variable ‘to’
Undefined global functions or variables:
  . from id iri parent text to
Consider adding
  importFrom("graphics", "text")
to your NAMESPACE file.
* 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 ‘OmicsMLRepoR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getMetadata
> ### Title: Download a harmonized metadata table
> ### Aliases: getMetadata
> 
> ### ** Examples
> 
> cmd <- getMetadata("cMD")
Error while performing HEAD request.
   Proceeding without cache information.
Warning: download failed
  web resource path: ‘https://zenodo.org/records/16458151/files/cMD_curated_metadata_release.csv’
  local file path: ‘/home/biocbuild/.cache/R/OmicsMLRepo/file290a1ad0a316f’
  reason: HTTP 503 Service Unavailable.
Warning: bfcdownload() failed
  rid: BFC1
  file: ‘https://zenodo.org/records/16458151/files/cMD_curated_metadata_release.csv’
  reason: download failed
Error: download failed; see warnings()
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:
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-tree_filter.R:4:1'): (code run outside of `test_that()`) ───────
  Error: download failed; see warnings()
  Backtrace:
      ▆
   1. └─OmicsMLRepoR::getMetadata("cMD") at test-tree_filter.R:4:1
   2.   └─OmicsMLRepoR:::s2p_cached_url(fpath)
   3.     ├─BiocFileCache::bfcdownload(bfc, rid = rid, ask = ask_on_update)
   4.     └─BiocFileCache::bfcdownload(bfc, rid = rid, ask = ask_on_update)
   5.       └─BiocFileCache:::.util_download_and_rename(...)
  
  [ FAIL 1 | WARN 4 | SKIP 0 | PASS 26 ]
  Error:
  ! Test failures.
  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 ‘Quickstart.Rmd’ using rmarkdown

Quitting from Quickstart.Rmd:61-64 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! download failed; see warnings()
---
Backtrace:
    ▆
 1. └─OmicsMLRepoR::getMetadata("cMD")
 2.   └─OmicsMLRepoR:::s2p_cached_url(fpath)
 3.     ├─BiocFileCache::bfcdownload(bfc, rid = rid, ask = ask_on_update)
 4.     └─BiocFileCache::bfcdownload(bfc, rid = rid, ask = ask_on_update)
 5.       └─BiocFileCache:::.util_download_and_rename(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'Quickstart.Rmd' failed with diagnostics:
download failed; see warnings()
--- failed re-building ‘Quickstart.Rmd’

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

Error: Vignette re-building failed.
Execution halted

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

Status: 3 ERRORs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/OmicsMLRepoR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL OmicsMLRepoR
###
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘OmicsMLRepoR’ ...
** this is package ‘OmicsMLRepoR’ version ‘1.5.5’
** using staged installation
** R
** data
** 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 (OmicsMLRepoR)

R version 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(OmicsMLRepoR)
> 
> test_check("OmicsMLRepoR")
Saving _problems/test-tree_filter-4.R
[ FAIL 1 | WARN 4 | SKIP 0 | PASS 26 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-tree_filter.R:4:1'): (code run outside of `test_that()`) ───────
Error: download failed; see warnings()
Backtrace:
    ▆
 1. └─OmicsMLRepoR::getMetadata("cMD") at test-tree_filter.R:4:1
 2.   └─OmicsMLRepoR:::s2p_cached_url(fpath)
 3.     ├─BiocFileCache::bfcdownload(bfc, rid = rid, ask = ask_on_update)
 4.     └─BiocFileCache::bfcdownload(bfc, rid = rid, ask = ask_on_update)
 5.       └─BiocFileCache:::.util_download_and_rename(...)

[ FAIL 1 | WARN 4 | SKIP 0 | PASS 26 ]
Error:
! Test failures.
Execution halted