[Bioc-devel] groHMM package error

[Mike Smith]

Dear Tulip,

The decideTestsDGE() function was deprecated in edgeR 4.2 and removed in
the new 4.4 release.  You can find some notes ion this n the NEWS at
https://bioconductor.org/packages/release/bioc/news/edgeR/NEWS

It looks  to me like you should be able to use decideTests() as a drop in
replacement in your package.

Best,
Mike

On Mon, 25 Nov 2024 at 23:23, Tulip Nandu <Tulip.Nandu using utsouthwestern.edu>
wrote:

> Hi,
>
> I keep getting this message from Bioconductor for groHMM package and don't
> know what the error is since I haven't changed anything in the package. Can
> someone please help?
>
> Regards,
> Tulip.
>
>
>
>
> "Warning in makeConsensusAnnotations(kgChr7, keytype = "gene_id", mc.cores
> = getOption("mc.cores")) :
>   562 ranges do not have gene_id and they are
>             dropped
> Reduce isoforms(701) ... OK
> Truncate overlapped ranges ... OK
>
> 'select()' returned 1:1 mapping between keys and columns
> Calculate overlapping ... OK
> Scale overlapping ... OK
> Warning: file stem
> ‘/home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpkfITSx/Rbuild130dca6dd2fd85/groHMM/vignettes/groHMM-fig2’
> is not portable
> Calculate overlapping ... OK
> Scale overlapping ... OK
> Loading required package: limma
>
> Attaching package: ‘limma’
>
> The following object is masked from ‘package:BiocGenerics’:
>
>     plotMA
>
>
> Error: processing vignette 'groHMM.Rnw' failed with diagnostics:
>  chunk 21 (label = DE for trascripts)
> Error in decideTestsDGE(et, p = 0.001, adjust = "fdr") :
>   could not find function "decideTestsDGE"
>
> --- failed re-building ‘groHMM.Rnw’
>
> SUMMARY: processing the following file failed:
>   ‘groHMM.Rnw’
>
> Error: Vignette re-building failed.
> Execution halted"
>
>
>
>
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