[Bioc-devel] possible ExperimentHub cache problem in the BBS with gDNAx

[Robert Castelo]

hi, yes, here they are:

library(ExperimentHub)
eh <- ExperimentHub()
ehres <- subset(eh, preparerclass == "gDNAinRNAseqData")
names(ehres)
[1] "EH8079" "EH8080" "EH8081" "EH8082" "EH8083" "EH8084" "EH8085" 
"EH8086" "EH8087"

should I bump again gDNAx to rebuild?

thanks,

robert.

On 20/6/25 17:13, Kern, Lori wrote:
> Can you provide the EH ids of the resources involved to reset?
>
> Lori Shepherd - Kern
>
> Bioconductor Core Team
>
> Roswell Park Comprehensive Cancer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
>
> ------------------------------------------------------------------------
> *From:* Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of 
> Robert Castelo via Bioc-devel <bioc-devel using r-project.org>
> *Sent:* Friday, June 20, 2025 11:11 AM
> *To:* bioc-devel using r-project.org <bioc-devel using r-project.org>
> *Subject:* [Bioc-devel] possible ExperimentHub cache problem in the 
> BBS with gDNAx
> Hi,
>
> I received the notice below about gDNAx devel failing in linux, here's
> the report:
>
> https://secure-web.cisco.com/1BzlfjF43Jl2RAQ7sz6-KkQG8OuVLCK9Io6YQ9n8ua3A9OXGhoHIf1iPW8iB5bjvNyt5NTuSWglO-_AR9o4umiYdvSPDL4gp73izY2XcJQdDOiPgrF4h7AmzzyXonwYVy_lW5lmVfq3adWRiBnmuH-aoHPu28Y8GDqh1KacY63xIhME9McZdV8up5BonDHPBe6eF-H6uhXoxvlbmLId_1Ti9RWABvCBVxzwzdLd2c9cs0h7-LLrVZqKjYW5TyilizNEdKTt4qxRXuFkLblLTaHamGkYN-kbm5_EuquuNjaDGSyw32ayGb771haTL2f6YO/https%3A%2F%2Fbioconductor.org%2FcheckResults%2Fdevel%2Fbioc-LATEST%2FgDNAx%2Fnebbiolo2-buildsrc.html
>
> the error seems to have something to do with loading data from the cache
> of the ExperimentHub when building the vignette. It does not happen in
> linux-aarch64 or in any other platform, and in release gives a similar
> error, but on the Windows platform:
>
> https://secure-web.cisco.com/18fFiAdfquiuJWqiYz7PnHd8ZeggBJM7COUazCm1MrVEjE624JIv4SMQs0MwrZZLTRFijJFBYNdWvh_ZrdjUbQziDNqOOxGNs-2YFlTLD-EKj0RY4oJBPaGeLieaAXDmCacrqZvpewyZuMXPMyOXYMYHOKE3DQmp-Ktc-UoFwV-WO7X56lb4Ml35YYBjj7BgC9nGFWgdVuVbStFS3kvb7q9c2tcNuq8jordqRAhaoYNB8PzMLEsWfqM8YhcXqwvenlVYmqhWHIMrtMfg1HOG8X9yeenlP_SFNbYet85btkuLVALKTRYQJleFWZ2JKbUAv/https%3A%2F%2Fbioconductor.org%2FcheckResults%2F3.21%2Fbioc-LATEST%2FgDNAx%2Fpalomino7-buildsrc.html
>
> while for linux and every other platform builds fine. This has been
> happening since we switched to the new release, I tried to bump the
> version in both, devel and release, but the error in these two specific
> platforms remains. Could we try to reset somehow the ExperimentHub cache
> in these two platforms for gDNAx? of course, if you have any other
> suggestion that I can try, please let me know.
>
> thanks!
>
> robert.
>
> -------- Forwarded Message --------
> Subject:         gDNAx Bioconductor package
> Date:    Fri, 20 Jun 2025 09:53:09 -0400
> From:    CoreTeam Bioconductor <bioconductorcoreteam using gmail.com>
> To: robert.castelo using upf.edu
>
>
>
> Hello Package Maintainer,
>
> We would like to bring to your attention that your package is failing in
> devel across all linux. This is very problematic. Please investigate the
> issues and fix the package to avoid deprecation.
>
> https://secure-web.cisco.com/1CNgAR8fLhWtx1zU-KjuZN9QKrNZOFgGI8M4Aqu0B3IENvm_iVh25oIMo2YMa7Vh-B91VzvapTbyfwd4bJ8qO4muJAr7baR5QZMjov2w84V75i7HPaXNzHwTcoeEaEejKNl8bjqgG4nOsUgBGbHFP3dnZqWdZUa8SfsRhpdK3JhxtKGg_oOdYmO-JLZCJR0l32xIHP3zW9tPPpHvv3F3CuCCKdhzOJ1tXY6vR8lImUFQmLRGSHyGyLZyp2XaLwZsz_7sSNSl2EuEVpaxKgXjejx062gDmsyMkRAG_yJ5XXu7G1niJy8UPhp4OmOxpkSOL/https%3A%2F%2Fbioconductor.org%2FcheckResults%2Fdevel%2Fbioc-LATEST%2F
>
> If you have further questions or concerns please reach out on the
> bioc-devel using r-project.org
>
> We appreciate your quick attention to this matter
>
> Cheers,
> On behalf of the Bioconductor Core Team
>
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-- 
Robert Castelo, PhD
Associate Professor
Dept. of Medicine and Life Sciences
Universitat Pompeu Fabra (UPF)
Barcelona Biomedical Research Park (PRBB)
Dr Aiguader 88
E-08003 Barcelona, Spain
telf: +34.933.160.514

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