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-boun...@r-project.org> on behalf of Robert Castelo via Bioc-devel <bioc-devel@r-project.org> Sent: Tuesday, June 24, 2025 11:19 AM To: Kern, Lori <lori.sheph...@roswellpark.org> Cc: bioc-devel@r-project.org <bioc-devel@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.cast...@upf.edu> > *Sent:* Friday, June 20, 2025 11:57 AM > *To:* Kern, Lori <lori.sheph...@roswellpark.org> > *Cc:* bioc-devel@r-project.org <bioc-devel@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-boun...@r-project.org> >> <mailto:bioc-devel-boun...@r-project.org> on behalf of Robert Castelo >> via Bioc-devel <bioc-devel@r-project.org> >> <mailto:bioc-devel@r-project.org> >> *Sent:* Friday, June 20, 2025 11:11 AM >> *To:* bioc-devel@r-project.org <mailto:bioc-devel@r-project.org> >> <bioc-devel@r-project.org> <mailto:bioc-devel@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 <bioconductorcoret...@gmail.com> >> <mailto:bioconductorcoret...@gmail.com> >> To: robert.cast...@upf.edu <mailto:robert.cast...@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@r-project.org <mailto:bioc-devel@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@r-project.org <mailto:Bioc-devel@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 >> 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. -- 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]] _______________________________________________ Bioc-devel@r-project.org mailing list https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/bioc-devel__;!!LRXxDv2l!TDBMGH5YyUrXE9_SjQfw7PJ-7qMGi-hvB2XY3dbUib1QpiRyqXtolSbZRpsDghN8fPV_5-LOWRuc42xcg3LuHIsJw1Z0eddC4w$ [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
