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://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><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://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<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://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]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
