[Bioc-devel] groHMM package error

Wed Dec 4 23:23:58 CET 2024

Hi,

Thank you for your earlier message.

tulipnandu using tulips-mbp groHMM % git remote -v
origin git using github.com:Kraus-Lab/groHMM.git (fetch)
origin git using github.com:Kraus-Lab/groHMM.git (push)
upstream git using git.bioconductor.org:packages/groHMM.git (fetch)
upstream git using git.bioconductor.org:packages/groHMM.git (push)

After that:

I keep getting this error message:

tulipnandu using tulips-mbp groHMM % ssh -T git using github.com

git using github.com: Permission denied (publickey).

I have added the key to the github account on BioHPC.

Another message I receive:

tulipnandu using tulips-mbp groHMM % git push origin master
git using github.com: Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
tulipnandu using tulips-mbp groHMM %

I have made the changes to the git repository at our end.

Can you please help me?

Regards,

Tulip.

________________________________
From: James W. MacDonald <jmacdon using uw.edu>
Sent: Tuesday, December 3, 2024 2:31 PM
To: Tulip Nandu <Tulip.Nandu using UTSouthwestern.edu>; Mike Smith <grimbough using gmail.com>
Cc: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: RE: [Bioc-devel] groHMM package error

You need to commit your changes to git using git.bioconductor.org, which you apparently have not done as yet (you should have git using git.bioconductor.org set up as a remote which you can see by doing git remote -v). The last commit is Jennifer Wokaty bumping the version for the last release:

/groHMM$ git log
commit a68457648cdef96ae2a8f40c484496e935d0fcb3 (HEAD -> devel, origin/master, origin/devel, origin/HEAD)
Author: J Wokaty <jennifer.wokaty using sph.cuny.edu>
Date:   Tue Oct 29 09:56:11 2024 -0400

    bump x.y.z version to odd y following creation of RELEASE_3_20 branch

You also need to bump the version number in order to get the new version to build. You also need to make changes to the RELEASE_3_20 branch if you want the fix to propagate to the release version of your package. Please see the git version control section of the development pages https://urldefense.com/v3/__https://contributions.bioconductor.org/git-version-control.html__;!!MznTZTSvDXGV0Co!D1Ec1At0koOWiqp-WDw8kmv5F2XS6u9FgDh9_6bOg6sahspYVpDQH4VMAWnhLzWraEuUptCNTFhuhD3a6ZVoPFJgJ1w$

-----Original Message-----
From: Bioc-devel <bioc-devel-bounces using r-project.org> On Behalf Of Tulip Nandu
Sent: Tuesday, December 3, 2024 3:14 PM
To: Mike Smith <grimbough using gmail.com>
Cc: bioc-devel using r-project.org
Subject: Re: [Bioc-devel] groHMM package error

Hi,

I edited the file based on Mike' s suggestion on the git page (image1) but doesn't seem to reflect when I clone the file using the git clone bioconductor package yet. Can someone confirm it will be done and nothing else I have to do from my end.

Let me know.

Regards,
Tulip.

________________________________
From: Mike Smith <grimbough using gmail.com>
Sent: Tuesday, November 26, 2024 2:50 AM
To: Tulip Nandu <Tulip.Nandu using UTSouthwestern.edu>
Cc: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] groHMM package error

EXTERNAL MAIL

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://urldefense.com/v3/__https://bioconductor.org/packages/release/bioc/news/edgeR/NEWS__;!!K-Hz7m0Vt54!ml36G27n5i71mmZqYh9kGx64fb8MnMWqcgTRb-IOUtzTvcuIr8z00917gwIae3eKB558z662Sqs-Iu35-pnRAO0wmBtwCQ$ <https://urldefense.com/v3/__https://bioconductor.org/packages/release/bioc/news/edgeR/NEWS__;!!MznTZTSvDXGV0Co!BCGS40g3d3SSGednQhbxHgpWzGAsYc9EsCe70-JZ9IXVg3a8PO-zA19gV1ChkR4Rh_ekHivdYDmFEO8pn_DJEQx-jd1t$>

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<mailto: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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