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

Mon Oct 28 22:25:07 CET 2024

Hi Tulip,

To resolve the build issue, you’ll need to remove the deprecated or 
defunct function from your package (decideTestsDGE), error below:

Error in decideTestsDGE(et, p = 0.001, adjust = "fdr") :
   could not find function "decideTestsDGE"

Since edgeR has removed or changed the function in question (as 
indicated by the commit link shared earlier), updating your code to work 
with the current version of edgeR should address the issue.

Please replace any calls to that function with updated code or an 
alternative method that is compatible with the latest edgeR version. 
After making these changes, you can commit and push your updates to 
Bioconductor.

Once you’ve updated the package, check the build report again in 24 
hours to confirm that the problem is resolved.

Let us know if you need further assistance!

Best regards,

Marcel

On 10/28/24 5:05 PM, Tulip Nandu wrote:
> 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$><https://urldefense.com/v3/__https:/bioconductor.org/checkResults/3.20/bioc-LATEST/groHMM/nebbiolo2-buildsrc.html__;!!MznTZTSvDXGV0Co!B3JaGl8USfJiPoEt4dV8iNDuJSinsunPZ74W0z4ErkhHUECAlubisgSf0oTKNALBakNL-xdRGnroijm-Ixdwy4zuJFwmCdE8Bb8$> <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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