[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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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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