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-----Original Message-----
From: Bioc-devel <[email protected]> On Behalf Of
Hiranyamaya Dash
Sent: Tuesday, September 23, 2025 9:27 AM
To: [email protected]
Cc: Skene, Nathan G <[email protected]>; [email protected]
Subject: [Bioc-devel] ExperimentHub Package Error - C stack usage (R, BioC
devel)
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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"]]
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