Re: [Bioc-devel] news on tidybulk?

Hello, tidybulk passed all checks now. Sorry I was waiting for a response to my answer to a reviewer's question before sending updated versions, it was the wrong strategy. Please let me know if anything else is needed. Best wishes. *Stefano * Stefano Mangiola | Postdoctoral fellow

Re: [Bioc-devel] news on tidybulk?

Hello, I have asked advise for a quite mysterious error in Windows and I have been told to wait, and I did not receive further reply. And I received a positive feedback dvantwisk commented 13 days ago

[Bioc-devel] Problem updating Bioconductor package

Hi, We followed the instruction (https://bioconductor.org/developers/how-to/git/maintain-bioc-only/) to update a Bioconductor package. All went well until the last step (git push upstream master). The error message: FATAL: W any packages/MethylMix ogevaert DENIED by fallthru (or you

Re: [Bioc-devel] Python dependency

It's important to ask 'why Bioconductor?' with the answer partly involving interoperability with other Bioconductor packages and data representations (e.g., http://bioconductor.org/developers/how-to/commonMethodsAndClasses/). There wouldn't be much value in making something that is essentially

Re: [Bioc-devel] Python dependency

Hi, Yes Bioconductor packages can depend on Python modules. This should only happen behind the scene and be transparent to the end user (i.e. the end user is not expected to interact directly with the Python module). You can use reticulate (from CRAN) directly or, even better, use basilisk

Re: [Bioc-devel] Trouble accessing packages

If you added your github id to the credentials app (which would provide access keys) you should try to access the git.bioconductor.org repository for your package. See the git help pages for linking to bioconductor git repository http://bioconductor.org/developers/how-to/git/ Lori Shepherd

[Bioc-devel] Trouble accessing packages

Hello, I am Enio Gjerga and I have recently been assigned the maintenance of the CNORfeeder and CNORode packages. I have recently got the news that CNORfeeder have been having troubles which I intend to fix. Also I intend to update both of the packages with a few new features. However, I am

Re: [Bioc-devel] Trouble accessing packages

P.S. I have submitted my GitHub id to Bioconductor (enio23) but not sure how to proceed any further with this. Thanks again. On Tue, 24 Mar 2020 at 17:38, Enio Gjerga wrote: > Hello, > > I am Enio Gjerga and I have recently been assigned the maintenance of the > CNORfeeder and CNORode

Re: [Bioc-devel] Help needed on BioC Git credential for package maintainer

Hi I've created the account for you. I'll send you your login details in a private email. Nitesh > On Mar 24, 2020, at 12:20 PM, Huang, Lei [CRI] > wrote: > > Dear Bioconductor team, > > I am one of the maintainers of BioC packages Lumi >

[Bioc-devel] Help needed on BioC Git credential for package maintainer

Dear Bioconductor team, I am one of the maintainers of BioC packages Lumi (https://bioconductor.org/packages/release/bioc/html/lumi.html) and methyAnalysis (https://bioconductor.org/packages/release/bioc/html/methyAnalysis.html); and would like to sync the bug-fix with the bioc-devel

[Bioc-devel] Python dependency

To whom it may concern, I would like to upload onto Bioconductor a package which is currently developed in python. I was wondering if Bioconductor supports python dependencies or if I should re-program the package in R exclusively. Is calling python from R using the package "reticulate"

Re: [Bioc-devel] Issue Reproducing BioC 3.11 COHCAP Error Message

Hi Lori, Thank you very much for your help! Sincerely, Charles From: Shepherd, Lori Sent: Tuesday, March 24, 2020 5:39 AM To: Charles Warden ; 'Martin Morgan' ; 'Alexey Sergushichev' Cc: 'bioc-devel@r-project.org' Subject: Re: [Bioc-devel] Issue Reproducing BioC 3.11 COHCAP Error Message

Re: [Bioc-devel] Issue Reproducing BioC 3.11 COHCAP Error Message

Thank you for your contributions to Bioconductor. We appreciate you fixing COHCAP. I will begin the deprecation process for sRAP; there is no further action needed. Cheers, Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics &

Re: [Bioc-devel] issue 1333 tscR package accepted

Sorry for the delay. We will look at moving accepted packages into the official Bioconductor repository over the next few days. Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New

Re: [Bioc-devel] news on tidybulk?

I think "header says it all" may be intended ... the question is whether it is accepted. since the package seems to be in error state I am not sure it can move forward at this time On Tue, Mar 24, 2020 at 8:22 AM Shepherd, Lori < lori.sheph...@roswellpark.org> wrote: > Is there a question

Re: [Bioc-devel] news on tidybulk?

I am weak on finding logs, but at https://github.com/Bioconductor/Contributions/issues?q=is%3Aissue+is%3Aopen+tidybulk I see the package is in an error state. Can you fix that? On Tue, Mar 24, 2020 at 7:31 AM Stefano Mangiola wrote: > > ___ >

Re: [Bioc-devel] news on tidybulk?

Is there a question here? Nothing came through in the body of the email? Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From:

[Bioc-devel] news on tidybulk?

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[Bioc-devel] issue 1333 tscR package accepted

Dear Bioconductor team The package "tscR" was accepted 12 days ago. I would like to know how long it takes to send additional information as indicated in the issue (Bioconductor github issue 1333). Thank you so much. best, Fernando ___

[Bioc-devel] issue 1333 tscR package accepted

Dear Bioconductor team The package "tscR" was accepted 12 days ago. I would like to know how long it takes to send additional information as indicated in the issue (Bioconductor github issue 1333). Thank you so much. best, Fernando ___