Build/check report for BioC 3.22 experimental data - BUILD results for curatedTBData on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"	4902
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 curatedTBData on nebbiolo2

To the developers/maintainers of the curatedTBData package:
- 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: curatedTBData

Version: 2.6.0

Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data curatedTBData

StartedAt: 2025-11-04 11:15:13 -0500 (Tue, 04 Nov 2025)

EndedAt: 2025-11-04 11:16:17 -0500 (Tue, 04 Nov 2025)

EllapsedTime: 64.6 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data curatedTBData
###
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* checking for file ‘curatedTBData/DESCRIPTION’ ... OK
* preparing ‘curatedTBData’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘curatedTBData.Rmd’ using rmarkdown

Quitting from curatedTBData.Rmd:102-105 [unnamed-chunk-1]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! failed to load resource
  name: EH6606
  title: GSE79362_assay_reprocess_hg19
  reason: 1 resources failed to download
---
Backtrace:
     ▆
  1. └─curatedTBData::curatedTBData("GSE79362", dry.run = FALSE, curated.only = FALSE)
  2.   └─base::lapply(...)
  3.     └─curatedTBData (local) FUN(X[[i]], ...)
  4.       └─curatedTBData (local) lapply_pb(dfSub$ah_id, function(y) suppressMessages(tbData[[y]]))
  5.         └─base::lapply(X, wrapper, ...)
  6.           └─curatedTBData (local) FUN(X[[i]], ...)
  7.             └─curatedTBData (local) FUN(...)
  8.               ├─base::suppressMessages(tbData[[y]])
  9.               │ └─base::withCallingHandlers(...)
 10.               ├─tbData[[y]]
 11.               └─tbData[[y]]
 12.                 └─ExperimentHub (local) .local(x, i, j = j, ...)
 13.                   ├─methods::callNextMethod(...)
 14.                   │ └─base::eval(call, callEnv)
 15.                   │   └─base::eval(call, callEnv)
 16.                   └─AnnotationHub (local) .nextMethod(...)
 17.                     └─AnnotationHub (local) .local(x, i, j = j, ...)
 18.                       └─AnnotationHub:::.Hub_get1(...)
 19.                         └─base::tryCatch(...)
 20.                           └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 21.                             └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 22.                               └─value[[3L]](cond)
 23.                                 └─base::tryCatch(...)
 24.                                   └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 25.                                     └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 26.                                       └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'curatedTBData.Rmd' failed with diagnostics:
failed to load resource
  name: EH6606
  title: GSE79362_assay_reprocess_hg19
  reason: 1 resources failed to download
--- failed re-building ‘curatedTBData.Rmd’

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

Error: Vignette re-building failed.
Execution halted