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://bioconductor.org/checkResults/devel/bioc-LATEST/EWCE/nebbiolo2-buildsrc.html
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]]
_______________________________________________
[email protected] mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
