Hello James, Thanks for your note. To clarify, this issue affects both EWCE and ewceData packages, which I maintain. The error comes from ExperimentHub resource loading in R-devel / Bioc-devel and is also breaking Bioconductor package builds (see EWCE build report I shared).
Since it impacts package functionality and Bioconductor checks, I think it fits here on bioc-devel. I also suspect it may be related to recent changes in core R or Bioconductor in the devel branch. Any guidance would be much appreciated. Kind regards, Hiru On Tue, Sep 23, 2025 at 2:32 PM James W. MacDonald <[email protected]> wrote: > 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 <[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) > > !-------------------------------------------------------------------| > 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, [email protected] 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$title, "\n reason: ", > conditionMessage(err), call. = FALSE)17. value[[3L]](cond)16. > tryCatchOne(expr, names, parentenv, handlers[[1L]])15. > tryCatchList(expr, classes, parentenv, handlers)14. > tryCatch({message("Error loading resource.", "\n attempting to > re-download")fls <- cache(getHub(class), config = config, progress = > progress,force = TRUE, verbose = verbose) ... 13. value[[3L]](cond)12. > tryCatchOne(expr, names, parentenv, handlers[[1L]])11. > tryCatchList(expr, classes, parentenv, handlers)10. tryCatch({fls <- > cache(getHub(class), config = config, progress = progress,force = force, > verbose = verbose).get1(class) ... 9. .Hub_get1(x[idx], force = force, > verbose = verbose, config = config,progress = progress)8. > .local(x, i, j = j, ...)7. .nextMethod(x, i, j, ..., force = force, > verbose = verbose, config = config,progress = progress)6. eval(call, > callEnv)5. eval(call, callEnv)4. callNextMethod(x, i, j, ..., force = > force, verbose = verbose,config = config, progress = progress)3. > .local(x, i, j = j, ...)2. hub[["EH5376"]]1. hub[["EH5376"]] > > [[alternative HTML version deleted]] > > _______________________________________________ > [email protected] mailing list > > https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/bioc-devel__;!!K-Hz7m0Vt54!jQRutwoDHKXBq8fF6ZtbSiO6_chW2E8Y9Hj22-GAfWALznyO7R4HMVEQdtitlM40dTmY0ug0v_A2QxzZLg$ > [[alternative HTML version deleted]] _______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
