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

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	R Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences"	4522
kjohnson3	macOS 13.7.7 Ventura	arm64	R Under development (unstable) (2026-03-01 r89506) -- "Unsuffered Consequences"	2847
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 AnnotationHub on kjohnson3

To the developers/maintainers of the AnnotationHub package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/AnnotationHub.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: AnnotationHub

Version: 4.1.0

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

StartedAt: 2026-03-09 15:21:06 -0400 (Mon, 09 Mar 2026)

EndedAt: 2026-03-09 15:21:24 -0400 (Mon, 09 Mar 2026)

EllapsedTime: 17.3 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 AnnotationHub
###
##############################################################################
##############################################################################


* checking for file ‘AnnotationHub/DESCRIPTION’ ... OK
* preparing ‘AnnotationHub’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘AnnotationHub-HOWTO.Rmd’ using rmarkdown

Quitting from AnnotationHub-HOWTO.Rmd:12-22 [style]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `library()`:
! there is no package called 'txdbmaker'
---
Backtrace:
    ▆
 1. ├─base::suppressPackageStartupMessages(...)
 2. │ └─base::withCallingHandlers(expr, packageStartupMessage = function(c) tryInvokeRestart("muffleMessage"))
 3. └─base::library(txdbmaker)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'AnnotationHub-HOWTO.Rmd' failed with diagnostics:
there is no package called 'txdbmaker'
--- failed re-building ‘AnnotationHub-HOWTO.Rmd’

--- re-building ‘AnnotationHub.Rmd’ using rmarkdown

Quitting from AnnotationHub.Rmd:148-150 [dm3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! failed to load resource
  name: AH15146
  title: dm1ToDm2.over.chain.gz
  reason: require("rtracklayer") failed: use BiocManager::install() to install package?
---
Backtrace:
     ▆
  1. ├─dm[["AH15146"]]
  2. └─dm[["AH15146"]]
  3.   └─AnnotationHub (local) .local(x, i, j = j, ...)
  4.     └─AnnotationHub:::.Hub_get1(...)
  5.       └─base::tryCatch(...)
  6.         └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  7.           └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
  8.             └─value[[3L]](cond)
  9.               └─base::tryCatch(...)
 10.                 └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 11.                   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 12.                     └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'AnnotationHub.Rmd' failed with diagnostics:
failed to load resource
  name: AH15146
  title: dm1ToDm2.over.chain.gz
  reason: require("rtracklayer") failed: use BiocManager::install() to install package?
--- failed re-building ‘AnnotationHub.Rmd’

--- re-building ‘TroubleshootingTheHubs.Rmd’ using rmarkdown
--- finished re-building ‘TroubleshootingTheHubs.Rmd’

SUMMARY: processing the following files failed:
  ‘AnnotationHub-HOWTO.Rmd’ ‘AnnotationHub.Rmd’

Error: Vignette re-building failed.
Execution halted