[Bioc-devel] ExperimentHub Package Error - C stack usage (R, BioC devel)

[James W. MacDonald]

This list is meant for developers to discuss issues with package development. For general usage support, please post on the support site at https://support.bioconductor.org

-----Original Message-----
From: Bioc-devel <bioc-devel-bounces using r-project.org> On Behalf Of Hiranyamaya Dash
Sent: Tuesday, September 23, 2025 9:27 AM
To: bioc-devel using r-project.org
Cc: Skene, Nathan G <n.skene using imperial.ac.uk>; h.dash using imperial.ac.uk
Subject: [Bioc-devel] ExperimentHub Package Error - C stack usage (R, BioC devel)

!-------------------------------------------------------------------|
  This Message Is From an Untrusted Sender
  You have not previously corresponded with this sender.
  See https://itconnect.uw.edu/email-tags for additional information. 
  Please contact the UW-IT Service Center, help using uw.edu 206.221.5000,
  for assistance.
|-------------------------------------------------------------------!

Dear BioConductor Community,

I am writing to report a technical issue I have encountered when attempting to load ExperimentHub object "EH5376" from the ewceData package.

*Problem Description:*
When attempting to load the specified resource, I consistently receive a "C stack usage too close to the limit" error. This issue is NOT present in the release R and Bioc versions.

*Reprex:*
(bioc-devel, R 2025-08-22 r88678)

*Method 1: Loading via data package*

> ewceData::ctd()see ?ewceData and browseVignettes('ewceData') for 
> documentationloading from cacheError loading resource. attempting to 
> re-downloaddownloading 1 resourcesretrieving 1 resourceloading from 
> cacheError: failed to load resource  name: EH5376  title: ctd  reason: 
> C stack usage 7957312 is too close to the limit


*Method 2: Loading directly with ExperimentHub*

> hub <- ExperimentHub::ExperimentHub()snapshotDate(): 2025-09-22> 
> hub[["EH5376"]]see ?ewceData and browseVignettes('ewceData') for 
> documentationloading from cacheError loading resource. attempting to 
> re-downloaddownloading 1 resourcesretrieving 1 resourceloading from 
> cacheError: failed to load resource  name: EH5376  title: ctd  reason: 
> C stack usage 7953728 is too close to the limit


*Additional Context:*
I have verified that the package functions correctly when using the
*bioconductor_docker:RELEASE_3_19* image. No modifications have been made to the data or codebase ever since.

This error is also affecting the BioConductor build checks for packages that depend on this data resource. Specifically, the issue manifests in R-devel, BioC 3.22 build results, as evidenced in the EWCE package check
results:
https://urldefense.com/v3/__https://bioconductor.org/checkResults/devel/bioc-LATEST/EWCE/nebbiolo2-buildsrc.html__;!!K-Hz7m0Vt54!jQRutwoDHKXBq8fF6ZtbSiO6_chW2E8Y9Hj22-GAfWALznyO7R4HMVEQdtitlM40dTmY0ug0v_B27zPZDg$ 

I have prepared a complete traceback, attached below.

I would be most grateful for any assistance you could provide in resolving this issue.

Yours sincerely,
Hiru

--

*Hiranyamaya (Hiru) Dash* (he/him)

Research Assistant in Computational Genomics UK Dementia Research Institute at Imperial College London


---

Error: failed to load resource  name: EH5376  title: ctd  reason: C stack usage  7953728 is too close to the limit18. stop("failed to load resource", "\n name: ", names(x), "\n title: ",x$title, "\n reason: ", conditionMessage(err), call. = FALSE)17. value[[3L]](cond)16.
tryCatchOne(expr, names, parentenv, handlers[[1L]])15.
tryCatchList(expr, classes, parentenv, handlers)14.
tryCatch({message("Error loading resource.", "\n attempting to re-download")fls <- cache(getHub(class), config = config, progress = progress,force = TRUE, verbose = verbose) ... 13. value[[3L]](cond)12.
tryCatchOne(expr, names, parentenv, handlers[[1L]])11.
tryCatchList(expr, classes, parentenv, handlers)10. tryCatch({fls <- cache(getHub(class), config = config, progress = progress,force = force, verbose = verbose).get1(class) ... 9. .Hub_get1(x[idx], force = force, verbose = verbose, config = config,progress = progress)8.
.local(x, i, j = j, ...)7. .nextMethod(x, i, j, ..., force = force, verbose = verbose, config = config,progress = progress)6. eval(call, callEnv)5. eval(call, callEnv)4. callNextMethod(x, i, j, ..., force = force, verbose = verbose,config = config, progress = progress)3.
.local(x, i, j = j, ...)2. hub[["EH5376"]]1. hub[["EH5376"]]

	[[alternative HTML version deleted]]

_______________________________________________
Bioc-devel using r-project.org mailing list
https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/bioc-devel__;!!K-Hz7m0Vt54!jQRutwoDHKXBq8fF6ZtbSiO6_chW2E8Y9Hj22-GAfWALznyO7R4HMVEQdtitlM40dTmY0ug0v_A2QxzZLg$