[Bioc-devel] EXTERNAL: R: release of new version of package

[Jeroen Gilis]

Hi everyone,

I have a related question that could be relevant to the original poster.

Concrete example; the Bioconductor satuRn package http://bioconductor.org/packages/release/bioc/html/satuRn.html that I am maintaining. It was first released in RELEASE_3_13, so that was version 1.1.0 both on my Git and Bioconductor. For RELEASE_3_14, I did not actively follow up the package, resulting in a current package version of 1.1.0 on git, 1.2.0 on bioc 3.14 and 1.3.0 on bioc devel. I now want to update the package. Does this mean I have to jump from version 1.1.0 on my git to 1.3.1 in my git (and bioc devel) to propagate these changes to bioc devel?

Kind regards,


Jeroen Gilis


________________________________
From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Marcel Ramos <marcel.ramosperez using roswellpark.org>
Sent: Monday, December 20, 2021 8:02 PM
To: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] EXTERNAL: R: release of new version of package

Hi Emanuela,

You should not be pushing new features to the RELEASE_3_14 branch.
This is meant to be stable throughout the course of the release cycle.

Make sure you are pushing your new commits to the devel branch of
Bioconductor with:

      git push upstream master

Based on your git history, it looks like you were able to make changes.

Do not forget to bump the Z version of your package, e.g.,

1.5.1

in devel so that the new version of the package propagates. This can
take between 24 - 48 hours.

Best regards,

Marcel

On 12/20/21 1:43 PM, Emanuela Iovino wrote:
> Dear Nitesh
> thank you for your answer.
>   I followed Bioconductor instruction but when I pushed on
>
> upstream/RELEASE_3_14 I received always  Everything up-to-date.
>
> Before to follow Bioconductor instruction I already had pushed all my modification on my Github repository and I don't know if it  got me a problem in next steps.
>
> I checked the last commit onhttps://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fbioconductor.org%2FcheckResults%2Frelease%2Fbioc-LATEST%2FuncoverappLib%2F&data=04%7C01%7Cjeroen.gilis%40ugent.be%7C271fc28226574a4ba0d708d9c3eb6540%7Cd7811cdeecef496c8f91a1786241b99c%7C1%7C0%7C637756238053093335%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=pWDS9dMrj03KscaX%2FXvEmzt9IfZFjcS0bsTTlYDhgYs%3D&reserved=0  and it doesn't match with my last modification.
>
> Have I to repeat all steps?
>
> Thanks
>
> Emanuela
>
>
>
> ________________________________
> Da: Nitesh Turaga<nturaga.bioc using gmail.com>
> Inviato: luned� 20 dicembre 2021 15:36
> A: Emanuela Iovino<emanuela.iovino using unibo.it>
> Cc:bioc-devel using r-project.org  <bioc-devel using r-project.org>
> Oggetto: Re: [Bioc-devel] release of new version of package
>
> Hi,
>
> You�ll want these two tutorials since I�m guessing you have a Github Repo and along with the git.bioconductor repo.
>
> So you�ll first have to sync (1), then push your updates to both Github and Bioc server(2)
>
> (1)https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fbioconductor.org%2Fdevelopers%2Fhow-to%2Fgit%2Fsync-existing-repositories%2F&data=04%7C01%7Cjeroen.gilis%40ugent.be%7C271fc28226574a4ba0d708d9c3eb6540%7Cd7811cdeecef496c8f91a1786241b99c%7C1%7C0%7C637756238053093335%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=rvYzIfbIe%2FBe9SZ7ZN1s6%2BRBK7yYU90bWX1ONiZE4K0%3D&reserved=0
>
> (2)https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbioconductor.org%2Fdevelopers%2Fhow-to%2Fgit%2Fpush-to-github-bioc%2F&data=04%7C01%7Cjeroen.gilis%40ugent.be%7C271fc28226574a4ba0d708d9c3eb6540%7Cd7811cdeecef496c8f91a1786241b99c%7C1%7C0%7C637756238053093335%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=6b1EA%2Bo0eUCUGzkLlMgfuhlm3q3vrN4qmSbmqCyNxHg%3D&reserved=0
>
> Best
>
> Nitesh Turaga
> Scientist II, Department of Data Science,
> Bioconductor Core Team Member
> Dana Farber Cancer Institute
>
>> On Dec 20, 2021, at 9:32 AM, Emanuela Iovino<emanuela.iovino using unibo.it>  wrote:
>>
>> Hello everyone
>> I'm the developer and the maintainer of Bioconductor package uncoverappLib .
>> I recently added some features to package and I would like to know how update to Biocondunctor . Do I follow new package workflow ? (https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbioconductor.org%2Fdevelopers%2Fhow-to%2Fgit%2Fnew-package-workflow%2F&data=04%7C01%7Cjeroen.gilis%40ugent.be%7C271fc28226574a4ba0d708d9c3eb6540%7Cd7811cdeecef496c8f91a1786241b99c%7C1%7C0%7C637756238053093335%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=j2z7cyT6guPZBiTRFFsUO7I6S0T2JMNLSsP69EYsrIw%3D&reserved=0).
>> Many thanks in advance
>>
>> Emanuela Iovino
>> PhD Student in Data Science and Computation
>> Division of Medical Genetics
>> Dept. Medical and Surgical Sciences - DIMEC
>> University of Bologna
>> Pol.S.Orsola-Malpighi, via Massarenti 9,
>>
>>
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---
Marcel Ramos
Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Dept. of Biostatistics & Bioinformatics
Elm St. & Carlton St.
Buffalo, New York 14263


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