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

Tue Jul 1 12:25:48 CEST 2025

Andres, Lori,

Everything looks fine for gDNAx on the last report of the release and 
the devel builder, except for a TIMEOUT while checking examples in the 
devel build of taishan (aarch64), but which doesn't seem to be related 
to the ExperimentHub cache problem, so hopefully at some point it will 
go away by itself.

Thanks for your help!

robert.

On 6/25/25 19:53, Andres Wokaty wrote:
> Hi Robert,
>
> I've redownloaded the resources on the windows release builder. We 
> should see the result next week.
>
> Andres Wokaty (they/them)
>
> Waldron Lab at CUNY SPH
> Bioconductor Core Team
> ------------------------------------------------------------------------
> *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:* Tuesday, June 24, 2025 11:19 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
> * This email originates from a sender outside of CUNY. Verify the 
> sender before replying or clicking on links and attachments. *
>
> Hi,
>
> Thanks Lori, the error has disappeared from the devel build, but it is
> still there in the Windows release build, did you redownloaded the
> resources for the Windows release build as well?
>
> Thanks again!
>
> robert.
>
> On 20/6/25 12:13, Kern, Lori wrote:
> > 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 
> <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 <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 
> <mailto:bioc-devel using r-project.org>>
> >> <bioc-devel using r-project.org> <mailto: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://urldefense.com/v3/__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__;JSUlJSUlJSU!!LRXxDv2l!TDBMGH5YyUrXE9_SjQfw7PJ-7qMGi-hvB2XY3dbUib1QpiRyqXtolSbZRpsDghN8fPV_5-LOWRuc42xcg3LuHIsJw1bbrbHepA$
> >> 
> <https://urldefense.com/v3/__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__;JSUlJSUlJSU!!LRXxDv2l!TDBMGH5YyUrXE9_SjQfw7PJ-7qMGi-hvB2XY3dbUib1QpiRyqXtolSbZRpsDghN8fPV_5-LOWRuc42xcg3LuHIsJw1bbrbHepA$ 
> >
> >>
> >> 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://urldefense.com/v3/__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__;JSUlJSUlJSU!!LRXxDv2l!TDBMGH5YyUrXE9_SjQfw7PJ-7qMGi-hvB2XY3dbUib1QpiRyqXtolSbZRpsDghN8fPV_5-LOWRuc42xcg3LuHIsJw1aced6g9w$
> >> 
> <https://urldefense.com/v3/__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__;JSUlJSUlJSU!!LRXxDv2l!TDBMGH5YyUrXE9_SjQfw7PJ-7qMGi-hvB2XY3dbUib1QpiRyqXtolSbZRpsDghN8fPV_5-LOWRuc42xcg3LuHIsJw1aced6g9w$ 
> >
> >>
> >> 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 
> <mailto:bioconductorcoreteam using gmail.com>>
> >> To: robert.castelo using upf.edu <mailto: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://urldefense.com/v3/__https://secure-web.cisco.com/1CNgAR8fLhWtx1zU-KjuZN9QKrNZOFgGI8M4Aqu0B3IENvm_iVh25oIMo2YMa7Vh-B91VzvapTbyfwd4bJ8qO4muJAr7baR5QZMjov2w84V75i7HPaXNzHwTcoeEaEejKNl8bjqgG4nOsUgBGbHFP3dnZqWdZUa8SfsRhpdK3JhxtKGg_oOdYmO-JLZCJR0l32xIHP3zW9tPPpHvv3F3CuCCKdhzOJ1tXY6vR8lImUFQmLRGSHyGyLZyp2XaLwZsz_7sSNSl2EuEVpaxKgXjejx062gDmsyMkRAG_yJ5XXu7G1niJy8UPhp4OmOxpkSOL/https*3A*2F*2Fbioconductor.org*2FcheckResults*2Fdevel*2Fbioc-LATEST*2F__;JSUlJSUlJQ!!LRXxDv2l!TDBMGH5YyUrXE9_SjQfw7PJ-7qMGi-hvB2XY3dbUib1QpiRyqXtolSbZRpsDghN8fPV_5-LOWRuc42xcg3LuHIsJw1brept36g$
> >> 
> <https://urldefense.com/v3/__https://secure-web.cisco.com/1CNgAR8fLhWtx1zU-KjuZN9QKrNZOFgGI8M4Aqu0B3IENvm_iVh25oIMo2YMa7Vh-B91VzvapTbyfwd4bJ8qO4muJAr7baR5QZMjov2w84V75i7HPaXNzHwTcoeEaEejKNl8bjqgG4nOsUgBGbHFP3dnZqWdZUa8SfsRhpdK3JhxtKGg_oOdYmO-JLZCJR0l32xIHP3zW9tPPpHvv3F3CuCCKdhzOJ1tXY6vR8lImUFQmLRGSHyGyLZyp2XaLwZsz_7sSNSl2EuEVpaxKgXjejx062gDmsyMkRAG_yJ5XXu7G1niJy8UPhp4OmOxpkSOL/https*3A*2F*2Fbioconductor.org*2FcheckResults*2Fdevel*2Fbioc-LATEST*2F__;JSUlJSUlJQ!!LRXxDv2l!TDBMGH5YyUrXE9_SjQfw7PJ-7qMGi-hvB2XY3dbUib1QpiRyqXtolSbZRpsDghN8fPV_5-LOWRuc42xcg3LuHIsJw1brept36g$ 
> >
> >>
> >> 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 
> <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 
> <mailto:Bioc-devel using r-project.org>> mailing list
> >> 
> https://urldefense.com/v3/__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__;JSUlJSUl!!LRXxDv2l!TDBMGH5YyUrXE9_SjQfw7PJ-7qMGi-hvB2XY3dbUib1QpiRyqXtolSbZRpsDghN8fPV_5-LOWRuc42xcg3LuHIsJw1a5i2cK-w$
> >> 
> <https://urldefense.com/v3/__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__;JSUlJSUl!!LRXxDv2l!TDBMGH5YyUrXE9_SjQfw7PJ-7qMGi-hvB2XY3dbUib1QpiRyqXtolSbZRpsDghN8fPV_5-LOWRuc42xcg3LuHIsJw1a5i2cK-w$ 
> >
> >>
> >>
> >> This email message may contain legally privileged and/or confidential
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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
> >
> > 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
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> > 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
>
>         [[alternative HTML version deleted]]
>
> _______________________________________________
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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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