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> on behalf of > Robert Castelo via Bioc-devel <bioc-devel@r-project.org> > *Sent:* Friday, June 20, 2025 11:11 AM > *To:* bioc-devel@r-project.org <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://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 <bioconductorcoret...@gmail.com> > To: 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://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@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 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 [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
