[Bioc-devel] groHMM package error

Thu Dec 5 12:50:57 CET 2024

So the command that fails:

git push origin master

If we break down the command, it loosely is saying push to the remote listed as origin to the branch designation master and I'm on a branch called master (implied)
Looking at your origin remote:
origin git using github.com:Kraus-Lab/groHMM.git

That is to your own or your labs github.  This has nothing to do with Bioconductor permissions but that on the github. You will have to look into how to resolve this on github.

The upstream remote is the Bioconductor location of the package.
upstream git using git.bioconductor.org:packages/groHMM.git

That being said,  what is the name of the branch you are locally on?
Based on the first call, I will assume master.  Bioconductor no longer uses a master branch.  Our default, devel branch is now named devel.  See https://contributions.bioconductor.org/branch-rename-faqs.html
if your local branch is master you would do something like the following to push to git.bioconductor.org

git push upstream master:devel

essentially reading:  push the changes to the remote listed as upstream. And push my local master branch to the remote devel branch.

Cheers,

Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Tulip Nandu <Tulip.Nandu using UTSouthwestern.edu>
Sent: Wednesday, December 4, 2024 5:23 PM
To: James W. MacDonald <jmacdon using uw.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

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://secure-web.cisco.com/16_v9KvAnSn5NTE4bTiw78EKac1H9ipCVrD15qZr6e0WzggraBQhvfCSIwCLL-NpPpZOxGuzdCoG2QFSZYXUfh02U187DGSNi9GMRoeItGMXmL8Pxv6E1PaofrESKPYKGpKLAAQRczRO1tuXb1oM7q8ahoI5VlJUWZ16K09Ns6efVylSfGwcX3p0elHPzeH8nJ3FihmzlQHBZDYp0wHTwfeGkDBzeGOnqCuaTo92X12THhrzDkwVex8p5FJhW38JXKuMXH9g3J2-jcnq_tqak_SBvoa5WjbL36eOfKKNQpyaUSLEOjiwh6OIg-mYmQ0yx/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fcontributions.bioconductor.org%2Fgit-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://secure-web.cisco.com/1l4IXc7KdLp5eV00Nm_hQoy6Gk6XDiPosw64Iwbq_av3U6heY7PCBd3SXPirzNs0zT0xlkKrDXTNUg6-MDVzYtGvJhGSgKT9tMzL7-YHa5U9uKytV3jkX6wqVpRApTsmDBIEGNQeRggFExswQF9YAQOiqgWbapncK3zYZuq4mZ8VBwR-RB09_MRo8JkVl2k8kR2EiRbXaRJUp3si4q4dW4OQv9UpxMlBjjSitWPhD_5whHeJlyKitOLE_fYlSSOGyOM35LDGnLtj9_Der0ckR7qNYmAvyiXsh0VbLmTx_fFfEpWupZK4dZNqV_k9MVmd7/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fbioconductor.org%2Fpackages%2Frelease%2Fbioc%2Fnews%2FedgeR%2FNEWS__;!!K-Hz7m0Vt54!ml36G27n5i71mmZqYh9kGx64fb8MnMWqcgTRb-IOUtzTvcuIr8z00917gwIae3eKB558z662Sqs-Iu35-pnRAO0wmBtwCQ$ <https://secure-web.cisco.com/1l4IXc7KdLp5eV00Nm_hQoy6Gk6XDiPosw64Iwbq_av3U6heY7PCBd3SXPirzNs0zT0xlkKrDXTNUg6-MDVzYtGvJhGSgKT9tMzL7-YHa5U9uKytV3jkX6wqVpRApTsmDBIEGNQeRggFExswQF9YAQOiqgWbapncK3zYZuq4mZ8VBwR-RB09_MRo8JkVl2k8kR2EiRbXaRJUp3si4q4dW4OQv9UpxMlBjjSitWPhD_5whHeJlyKitOLE_fYlSSOGyOM35LDGnLtj9_Der0ckR7qNYmAvyiXsh0VbLmTx_fFfEpWupZK4dZNqV_k9MVmd7/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fbioconductor.org%2Fpackages%2Frelease%2Fbioc%2Fnews%2FedgeR%2FNEWS__;!!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"

________________________________

UT Southwestern

Medical Center

The future of medicine, today.

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