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

[Tulip Nandu]

Hi,

Yes, I haven't change the master package. What is the solution? Also the link below is not working.

Regards,

Tulip.

________________________________
From: Marcel Ramos Pérez <marcel.ramosperez45 using login.cuny.edu>
Sent: Thursday, October 24, 2024 5:04 PM
To: bioc-devel using r-project.org <bioc-devel using r-project.org>; Tulip Nandu <Tulip.Nandu using UTSouthwestern.edu>
Subject: Re: [Bioc-devel] groHMM problems reported in the Multiple platform build/check report for BioC 3.20


Hi Tulip,

Are you sure? It looks like `edgeR` has deprecated / defunct that function. See this commit:

https://code.bioconductor.org/browse/edgeR/commit/bdd73bc0c6a0a710838f77ad419bdc2cf21ed357<https://urldefense.com/v3/__https://code.bioconductor.org/browse/edgeR/commit/bdd73bc0c6a0a710838f77ad419bdc2cf21ed357__;!!MznTZTSvDXGV0Co!FZyvCiEyFEAcLgnkBb2DTGMsmLnaxrPAyTLpU6UVmCjRBWUxO1z2PymsqtWVMqUcwpsIOr2JqPpmHYcELXPLhp7x7KBtkbwIOXlTurNykkGC$>

Best regards,

Marcel

On 10/24/24 5:56 PM, Tulip Nandu wrote:

* This email originates from a sender outside of CUNY. Verify the sender before replying or clicking on links and attachments. *

Hi,

Can someone guide me why this error came up. When there is no change to the package made.

Regards,
Tulip.


________________________________
From: Lee Kraus <Lee.Kraus using UTSouthwestern.edu><mailto:Lee.Kraus using UTSouthwestern.edu>
Sent: Thursday, October 24, 2024 1:16 PM
To: Tulip Nandu <Tulip.Nandu using UTSouthwestern.edu><mailto:Tulip.Nandu using UTSouthwestern.edu>
Subject: FW: groHMM problems reported in the Multiple platform build/check report for BioC 3.20






From: BBS-noreply using bioconductor.org<mailto:BBS-noreply using bioconductor.org> <BBS-noreply using bioconductor.org><mailto:BBS-noreply using bioconductor.org>
Date: Thursday, October 24, 2024 at 11:00 AM
To: Lee Kraus <Lee.Kraus using UTSouthwestern.edu><mailto: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!B3JaGl8USfJiPoEt4dV8iNDuJSinsunPZ74W0z4ErkhHUECAlubisgSf0oTKNALBakNL-xdRGnroijm-Ixdwy4zuJFwmCdE8Bb8$<https://urldefense.com/v3/__https:/bioconductor.org/checkResults/3.20/bioc-LATEST/groHMM/nebbiolo2-buildsrc.html__;!!MznTZTSvDXGV0Co!B3JaGl8USfJiPoEt4dV8iNDuJSinsunPZ74W0z4ErkhHUECAlubisgSf0oTKNALBakNL-xdRGnroijm-Ixdwy4zuJFwmCdE8Bb8$><https://urldefense.com/v3/__https:/bioconductor.org/checkResults/3.20/bioc-LATEST/groHMM/nebbiolo2-buildsrc.html__;!!MznTZTSvDXGV0Co!B3JaGl8USfJiPoEt4dV8iNDuJSinsunPZ74W0z4ErkhHUECAlubisgSf0oTKNALBakNL-xdRGnroijm-Ixdwy4zuJFwmCdE8Bb8$>

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

Notes:

  * This was the status of your package at the time this email was sent to you.
    Given that the online report is updated daily (in normal conditions) you
    could see something different when you visit the URL(s) above, especially if
    you do so several days after you received this email.

  * It is possible that the problems reported in this report are false positives,
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