[Bioc-devel] Build fails for Moonlight2R
Dear Lori, Thank you, I?ll keep an eye on the build reports and let you know 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.Shepherd at RoswellPark.org> Date: Thursday, 29 August 2024 at 17.06 To: bioc-devel at r-project.org <bioc-devel at r-project.org>, Matteo Tiberti <tiberti at 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-bounces at r-project.org> on behalf of Matteo Tiberti via Bioc-devel <bioc-devel at r-project.org>
Sent: Thursday, August 29, 2024 10:56 AM
To: bioc-devel at r-project.org <bioc-devel at r-project.org>
Subject: [Bioc-devel] Build fails for Moonlight2R
Sent: Thursday, August 29, 2024 10:56 AM
To: bioc-devel at r-project.org <bioc-devel at 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
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