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

Fri Jun 20 18:13:00 CEST 2025

I just redownloaded all listed ids.  Let's see what happens on the next build

Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Robert Castelo <robert.castelo using upf.edu>
Sent: Friday, June 20, 2025 11:57 AM
To: Kern, Lori <Lori.Shepherd using RoswellPark.org>
Cc: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] possible ExperimentHub cache problem in the BBS with gDNAx

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><mailto:bioc-devel-bounces using r-project.org> on behalf of Robert Castelo via Bioc-devel <bioc-devel using r-project.org><mailto:bioc-devel using r-project.org>
Sent: Friday, June 20, 2025 11:11 AM
To: bioc-devel using r-project.org<mailto:bioc-devel using r-project.org> <bioc-devel using r-project.org><mailto: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><mailto:bioconductorcoreteam using gmail.com>
To:      robert.castelo using upf.edu<mailto: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<mailto:bioc-devel using r-project.org>

We appreciate your quick attention to this matter

Cheers,
On behalf of the Bioconductor Core Team

        [[alternative HTML version deleted]]

_______________________________________________
Bioc-devel using r-project.org<mailto:Bioc-devel using r-project.org> mailing list
https://secure-web.cisco.com/1RQb--mv4APVjaft63uujELb1ZLVwwsxz72s3XjiV05DzYjX_0lYwC84FkVz_uSySNTzQbzStosyXZO6Q_iSNba9Jow3tfgKps5j9SqvJ5Webot95NijvPFQuyGMXgQJgZ5aML2Gx3Koo2McHEcM9KZCb5Khpc1KHVs-7bK9zx-Hdg5LerYIWHhRJznjFxCDfbigsO_eorhdADnOB8FPzGBQukuaCsGvOJdRltBJ_elmGS6-cfM3ih-I67ryoMESqgHJ-lyY9FA8stMEVdzDVTanhe6KnLVrcIccaXDmS1koXtdqZHrTunlfpmKblv96N/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel

This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.

--
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

This email message may contain legally privileged and/or confidential information.  If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited.  If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.
	[[alternative HTML version deleted]]