Multiple platform build/check report for BioC 3.23 - BUILD results for bedbaser on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"	4808
kjohnson3	macOS 13.7.7 Ventura	arm64	R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"	4542
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

BUILD results for bedbaser on kjohnson3

To the developers/maintainers of the bedbaser package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/bedbaser.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: bedbaser

Version: 1.3.4

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data bedbaser

StartedAt: 2026-01-21 15:43:36 -0500 (Wed, 21 Jan 2026)

EndedAt: 2026-01-21 15:43:45 -0500 (Wed, 21 Jan 2026)

EllapsedTime: 9.1 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data bedbaser
###
##############################################################################
##############################################################################


* checking for file ‘bedbaser/DESCRIPTION’ ... OK
* preparing ‘bedbaser’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘bedbaser.Rmd’ using rmarkdown
<!DOCTYPE html>
<!--[if lt IE 7]> <html class="no-js ie6 oldie" lang="en-US"> <![endif]-->
<!--[if IE 7]>    <html class="no-js ie7 oldie" lang="en-US"> <![endif]-->
<!--[if IE 8]>    <html class="no-js ie8 oldie" lang="en-US"> <![endif]-->
<!--[if gt IE 8]><!--> <html class="no-js" lang="en-US"> <!--<![endif]-->
<head>

<title>bedbase.org | 502: Bad gateway</title>
<meta charset="UTF-8" />
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta name="robots" content="noindex, nofollow" />
<meta name="viewport" content="width=device-width,initial-scale=1" />
<link rel="stylesheet" id="cf_styles-css" href="/cdn-cgi/styles/main.css" />
</head>
<body>
<div id="cf-wrapper">
    <div id="cf-error-details" class="p-0">
        <header class="mx-auto pt-10 lg:pt-6 lg:px-8 w-240 lg:w-full mb-8">
            <h1 class="inline-block sm:block sm:mb-2 font-light text-60 lg:text-4xl text-black-dark leading-tight mr-2">
                <span class="inline-block">Bad gateway</span>
                <span class="code-label">Error code 502</span>
            </h1>
            <div>
                Visit <a href="https://www.cloudflare.com/5xx-error-landing?utm_source=errorcode_502&utm_campaign=api.bedbase.org" target="_blank" rel="noopener noreferrer">cloudflare.com</a> for more information.
            </div>
            <div class="mt-3">2026-01-21 20:43:45 UTC</div>
        </header>
        <div class="my-8 bg-gradient-gray">
            <div class="w-240 lg:w-full mx-auto">
                <div class="clearfix md:px-8">
                    <div id="cf-browser-status" class=" relative w-1/3 md:w-full py-15 md:p-0 md:py-8 md:text-left md:border-solid md:border-0 md:border-b md:border-gray-400 overflow-hidden float-left md:float-none text-center">
  <div class="relative mb-10 md:m-0">
    
    <span class="cf-icon-browser block md:hidden h-20 bg-center bg-no-repeat"></span>
    <span class="cf-icon-ok w-12 h-12 absolute left-1/2 md:left-auto md:right-0 md:top-0 -ml-6 -bottom-4"></span>
    
  </div>
  <span class="md:block w-full truncate">You</span>
  <h3 class="md:inline-block mt-3 md:mt-0 text-2xl text-gray-600 font-light leading-1.3">
  
    Browser
  
  </h3>
  
  <span class="leading-1.3 text-2xl text-green-success">Working</span>
  
</div>
                    <div id="cf-cloudflare-status" class=" relative w-1/3 md:w-full py-15 md:p-0 md:py-8 md:text-left md:border-solid md:border-0 md:border-b md:border-gray-400 overflow-hidden float-left md:float-none text-center">
  <div class="relative mb-10 md:m-0">
    <a href="https://www.cloudflare.com/5xx-error-landing?utm_source=errorcode_502&#38;utm_campaign=api.bedbase.org" target="_blank" rel="noopener noreferrer">
    <span class="cf-icon-cloud block md:hidden h-20 bg-center bg-no-repeat"></span>
    <span class="cf-icon-ok w-12 h-12 absolute left-1/2 md:left-auto md:right-0 md:top-0 -ml-6 -bottom-4"></span>
    </a>
  </div>
  <span class="md:block w-full truncate">Ashburn</span>
  <h3 class="md:inline-block mt-3 md:mt-0 text-2xl text-gray-600 font-light leading-1.3">
  <a href="https://www.cloudflare.com/5xx-error-landing?utm_source=errorcode_502&utm_campaign=api.bedbase.org" target="_blank" rel="noopener noreferrer">
    Cloudflare
  </a>
  </h3>
  
  <span class="leading-1.3 text-2xl text-green-success">Working</span>
  
</div>
                    <div id="cf-host-status" class="cf-error-source relative w-1/3 md:w-full py-15 md:p-0 md:py-8 md:text-left md:border-solid md:border-0 md:border-b md:border-gray-400 overflow-hidden float-left md:float-none text-center">
  <div class="relative mb-10 md:m-0">
    
    <span class="cf-icon-server block md:hidden h-20 bg-center bg-no-repeat"></span>
    <span class="cf-icon-error w-12 h-12 absolute left-1/2 md:left-auto md:right-0 md:top-0 -ml-6 -bottom-4"></span>
    
  </div>
  <span class="md:block w-full truncate">api.bedbase.org</span>
  <h3 class="md:inline-block mt-3 md:mt-0 text-2xl text-gray-600 font-light leading-1.3">
  
    Host
  
  </h3>
  
  <span class="leading-1.3 text-2xl text-red-error">Error</span>
  
</div>
                </div>
            </div>
        </div>

        <div class="w-240 lg:w-full mx-auto mb-8 lg:px-8">
            <div class="clearfix">
                <div class="w-1/2 md:w-full float-left pr-6 md:pb-10 md:pr-0 leading-relaxed">
                    <h2 class="text-3xl font-normal leading-1.3 mb-4">What happened?</h2>
                    <p>The web server reported a bad gateway error.</p>
                </div>
                <div class="w-1/2 md:w-full float-left leading-relaxed">
                    <h2 class="text-3xl font-normal leading-1.3 mb-4">What can I do?</h2>
                    <p class="mb-6">Please try again in a few minutes.</p>
                </div>
            </div>
        </div>

        <div class="cf-error-footer cf-wrapper w-240 lg:w-full py-10 sm:py-4 sm:px-8 mx-auto text-center sm:text-left border-solid border-0 border-t border-gray-300">
    <p class="text-13">
      <span class="cf-footer-item sm:block sm:mb-1">Cloudflare Ray ID: <strong class="font-semibold">9c19a5492b18ef66</strong></span>
      <span class="cf-footer-separator sm:hidden">&bull;</span>
      <span id="cf-footer-item-ip" class="cf-footer-item hidden sm:block sm:mb-1">
        Your IP:
        <button type="button" id="cf-footer-ip-reveal" class="cf-footer-ip-reveal-btn">Click to reveal</button>
        <span class="hidden" id="cf-footer-ip">170.223.207.78</span>
        <span class="cf-footer-separator sm:hidden">&bull;</span>
      </span>
      <span class="cf-footer-item sm:block sm:mb-1"><span>Performance &amp; security by</span> <a rel="noopener noreferrer" href="https://www.cloudflare.com/5xx-error-landing?utm_source=errorcode_502&#38;utm_campaign=api.bedbase.org" id="brand_link" target="_blank">Cloudflare</a></span>
      
    </p>
    <script>(function(){function d(){var b=a.getElementById("cf-footer-item-ip"),c=a.getElementById("cf-footer-ip-reveal");b&&"classList"in b&&(b.classList.remove("hidden"),c.addEventListener("click",function(){c.classList.add("hidden");a.getElementById("cf-footer-ip").classList.remove("hidden")}))}var a=document;document.addEventListener&&a.addEventListener("DOMContentLoaded",d)})();</script>
  </div><!-- /.error-footer -->

    </div>
</div>
</body>
</html>
Quitting from bedbaser.Rmd:43-47 [bedbase]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! '.service_get_api_file' failed:
  Bad Gateway (HTTP 502).
---
Backtrace:
     ▆
  1. └─bedbaser::BEDbase(tempdir())
  2.   ├─base::suppressWarnings(...)
  3.   │ └─base::withCallingHandlers(...)
  4.   ├─bedbaser:::.BEDbase(...)
  5.   │ └─methods::new(`<chr>`, ...)
  6.   │   ├─methods::initialize(value, ...)
  7.   │   └─methods::initialize(value, ...)
  8.   └─AnVIL::Service(...)
  9.     └─AnVIL:::.service_get_api_file(api_reference_url, api_reference_headers)
 10.       └─AnVILBase::avstop_for_status(response, ".service_get_api_file")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'bedbaser.Rmd' failed with diagnostics:
'.service_get_api_file' failed:
  Bad Gateway (HTTP 502).
--- failed re-building ‘bedbaser.Rmd’

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

Error: Vignette re-building failed.
Execution halted