Skip to content

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

4 messages · Tulip Nandu, Marcel Ramos

#
Hi,

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

Regards,
Tulip.
#
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

Best regards,

Marcel
On 10/24/24 5:56 PM, Tulip Nandu wrote:
3 days later
#
Hi,

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

Regards,

Tulip.
#
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: