[Bioc-devel] groHMM problems reported in the Multiple platform build/check report for BioC 3.20

[Tulip Nandu]

Hi,

This was an error previously and I had received this response. Something form your end needs to be fixed.
"

Hi Tulip,

I think this is caused by a late change in S4Vectors: https://github.com/Bioconductor/S4Vectors/commit/15349ef40f141b16df6daf3e38f3782ef54eb60c<https://urldefense.com/v3/__https://github.com/Bioconductor/S4Vectors/commit/15349ef40f141b16df6daf3e38f3782ef54eb60c__;!!MznTZTSvDXGV0Co!Ao4I2ZtCvjQcoMRntfclNKhavdTUeBp4jd7TldBHrrdZCurg2cL4XQMceCPoCmnjeBJ-Vz392JdRWz7Ua6HwxmntqbbYqxDVcIBsOw$>

This was an attempt at implementing the following feature request: https://github.com/Bioconductor/DelayedArray/issues/108<https://urldefense.com/v3/__https://github.com/Bioconductor/DelayedArray/issues/108__;!!MznTZTSvDXGV0Co!Ao4I2ZtCvjQcoMRntfclNKhavdTUeBp4jd7TldBHrrdZCurg2cL4XQMceCPoCmnjeBJ-Vz392JdRWz7Ua6HwxmntqbbYqxA-heiWAw$>

Sorry that this change broken your subsetting operation kgChr7[de==1, ].

Honestly, it's hard (if not impossible) to anticipate that some code somewhere would use a Nx1 TestResults object (this is what 'de==1' is!) as a subscript to subset a Vector derivative like your GRanges object kgChr7. It was just luck that this was working so far. Anyways, I think we can make this work again. A patch is coming.

Best,

H.

"

Let me know if it solves the problem.

Regards,
Tulip.


________________________________
From: Lee Kraus <Lee.Kraus using UTSouthwestern.edu>
Sent: Monday, October 14, 2024 12:21 PM
To: Tulip Nandu <Tulip.Nandu using UTSouthwestern.edu>
Subject: FW: groHMM problems reported in the Multiple platform build/check report for BioC 3.20


Hi Tulip,



Can you take care of this?



Thanks,

Lee



From: BBS-noreply using bioconductor.org <BBS-noreply using bioconductor.org>
Date: Monday, October 14, 2024 at 11:00 AM
To: Lee Kraus <Lee.Kraus using UTSouthwestern.edu>
Subject: groHMM problems reported in the Multiple platform build/check report for BioC 3.20

EXTERNAL MAIL

[This is an automatically generated email. Please don't reply.]

Hi groHMM maintainer,

According to the Multiple platform build/check report for BioC 3.20,
the groHMM package has the following problem(s):

  o ERROR for 'R CMD build' on nebbiolo2. See the details here:
      https://urldefense.com/v3/__https://bioconductor.org/checkResults/3.20/bioc-LATEST/groHMM/nebbiolo2-buildsrc.html__;!!MznTZTSvDXGV0Co!DWD5B_llxewe3VjmZ6uDo-t00Eujz9p2zNf7XsZwGbHutJXGhSUa52MrL_T2CospM5XOb9HacJHoGa1Zr5q1M1hz6Jf7lRCbx3o$<https://urldefense.com/v3/__https:/bioconductor.org/checkResults/3.20/bioc-LATEST/groHMM/nebbiolo2-buildsrc.html__;!!MznTZTSvDXGV0Co!DWD5B_llxewe3VjmZ6uDo-t00Eujz9p2zNf7XsZwGbHutJXGhSUa52MrL_T2CospM5XOb9HacJHoGa1Zr5q1M1hz6Jf7lRCbx3o$>

Please take the time to address this by committing and pushing
changes to your package at git.bioconductor.org

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