[Bioc-devel] Build fails for Moonlight2R

Wed Sep 4 13:02:43 CEST 2024

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

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From: Kern, Lori <Lori.Shepherd using RoswellPark.org>
Date: Thursday, 29 August 2024 at 17.06
To: bioc-devel using r-project.org <bioc-devel using r-project.org>, Matteo Tiberti <tiberti using 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 using r-project.org> on behalf of Matteo Tiberti via Bioc-devel <bioc-devel using r-project.org>
Sent: Thursday, August 29, 2024 10:56 AM
To: bioc-devel using r-project.org <bioc-devel using 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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