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:
�w�w Error ('test-DMA.R:14:1'): (code run outside of `test_that()`)
�w�w�w�w�w�w�w�w�w�w�w�w�w�w
Error: failed to load resource
name: AH14150
title: hg19ToHg38.over.chain.gz
reason: expected 11 elements in header, got 1, on line 8
Backtrace:
�g
1. �|�wMoonlight2R::DMA(...) at test-DMA.R:14:1
2. �|�wMoonlight2R::LiftMAF(Infile = DEGs_mut_annotated_19, Current_Build =
"GRCh37")
3. �u�wah[["AH14150"]]
4. �|�wah[["AH14150"]]
5. �|�wAnnotationHub (local) .local(x, i, j = j, ...)
6. �|�wAnnotationHub:::.Hub_get1(x[idx], force = force, verbose =
verbose)
7. �|�wbase::tryCatch(...)
8. �|�wbase (local) tryCatchList(expr, classes, parentenv,
handlers)
9. �|�wbase (local) tryCatchOne(expr, names, parentenv,
handlers[[1L]])
10. �|�wvalue[[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] 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
�V a part of the Danish Cancer Society
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