Dear Lori, The reset seems to have worked – we are now all green in both release and devel
Thanks again for your help Best, Matteo Tiberti Danish Cancer Institute Strandboulevarden 49 DK-2100 Copenhagen Telephone: +45 35 25 73 07 – a part of the Danish Cancer Society [An image showing the Danish Cancer Society's name and logo called the bow in red font. Displayed in red]<https://www.cancer.dk/?utm_source=email&utm_medium=medarbejderemail&utm_campaign=medarbejderemail&utm_content=cancerdk> www.cancer.dk<https://www.cancer.dk/international/> | Our privacy policy<https://www.cancer.dk/om-os/privatlivspolitik/> From: Kern, Lori <lori.sheph...@roswellpark.org> Date: Thursday, 29 August 2024 at 17.06 To: bioc-devel@r-project.org <bioc-devel@r-project.org>, Matteo Tiberti <tibe...@cancer.dk> Subject: Re: Build fails for Moonlight2R Thank you for letting us know. We will reset the resource on the windows machine to see if that helps. 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 Matteo Tiberti via Bioc-devel <bioc-devel@r-project.org> Sent: Thursday, August 29, 2024 10:56 AM To: bioc-devel@r-project.org <bioc-devel@r-project.org> Subject: [Bioc-devel] Build fails for Moonlight2R Dear maintainers, we've been having a build fail on Palomino7 (Windows builder) for our Moonlight2R package release branch (3.19), one of our tests fails. I cannot reproduce this fail locally and looks like it might be an issue with data from AnnotationHub: ── Error ('test-DMA.R:14:1'): (code run outside of `test_that()`) ────────────── Error: failed to load resource name: AH14150 title: hg19ToHg38.over.chain.gz reason: expected 11 elements in header, got 1, on line 8 Backtrace: ▆ 1. └─Moonlight2R::DMA(...) at test-DMA.R:14:1 2. └─Moonlight2R::LiftMAF(Infile = DEGs_mut_annotated_19, Current_Build = "GRCh37") 3. ├─ah[["AH14150"]] 4. └─ah[["AH14150"]] 5. └─AnnotationHub (local) .local(x, i, j = j, ...) 6. └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose) 7. └─base::tryCatch(...) 8. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 9. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 10. └─value[[3L]](cond) Similarly, in the same Moonlight2R package and devel version (3.20), we have a fail on Kunpeng2 in one of the examples which might depend on the runner (or on the fact that the NCBI ftp might have been down), as I cannot reproduce it locally either:
dataGEO <- getDataGEO(GEOobject = "GSE15641", platform = "GPL96")
Error in open.connection(x, "rb") : Timeout was reached: [ftp.ncbi.nlm.nih.gov<ftp.ncbi.nlm.nih.gov>] Resolving timed out after 10000 milliseconds Calls: getDataGEO ... getAndParseGSEMatrices -> getDirListing -> <Anonymous> -> read_html.default Execution halted For the latter, it is possible we just might need to wait for the next test round, but I thought I’d mention just in case. If you could please advise or have a look, it would be very appreciated. Thank you and kind regards, Matteo Tiberti Danish Cancer Institute Strandboulevarden 49 DK-2100 Copenhagen Telephone: +45 35 25 73 07 – a part of the Danish Cancer Society [An image showing the Danish Cancer Society's name and logo called the bow in red font. 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