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

[Jeroen Gilis]

Thank you for the quick reply, Robert, this indeed answered my question.

Kind regards,

Jeroen
________________________________
From: Robert M. Flight <rflight79 using gmail.com>
Sent: Thursday, December 23, 2021 12:58 PM
To: Jeroen Gilis <Jeroen.Gilis using UGent.be>
Cc: bioc-devel <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] EXTERNAL: R: release of new version of package

Jeroen,

Yes, you will have to move up that version number.

However, the way to do that is to

git pull upstream master

This will bring in the changes that have been made to version numbers by the Bioconductor team.

If you don't do the pull first, you will likely get error messages and conflicts when you make your changes.

After the pull and merge, THEN start making your changes you want to make, and push those to both GitHub and Bioconductor.

Hope that helps.

Robert


On Thu, Dec 23, 2021, 5:29 AM Jeroen Gilis <Jeroen.Gilis using ugent.be<mailto:Jeroen.Gilis using ugent.be>> wrote:
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<https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fbioconductor.org%2Fpackages%2Frelease%2Fbioc%2Fhtml%2FsatuRn.html&data=04%7C01%7Cjeroen.gilis%40ugent.be%7Cf7a035a7ca3a4680bd6d08d9c60b8245%7Cd7811cdeecef496c8f91a1786241b99c%7C1%7C0%7C637758575012377269%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=%2BRqbjtjQHFj%2BUzfw8nu3iYNe7baUcMVZF0NAACjb64Q%3D&reserved=0> 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<mailto:bioc-devel-bounces using r-project.org>> on behalf of Marcel Ramos <marcel.ramosperez using roswellpark.org<mailto:marcel.ramosperez using roswellpark.org>>
Sent: Monday, December 20, 2021 8:02 PM
To: bioc-devel using r-project.org<mailto:bioc-devel using r-project.org> <bioc-devel using r-project.org<mailto: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<http://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<mailto:nturaga.bioc using gmail.com>>
> Inviato: luned� 20 dicembre 2021 15:36
> A: Emanuela Iovino<emanuela.iovino using unibo.it<mailto:emanuela.iovino using unibo.it>>
> Cc:bioc-devel using r-project.org<mailto:Cc%3Abioc-devel using r-project.org>  <bioc-devel using r-project.org<mailto: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<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%7Cf7a035a7ca3a4680bd6d08d9c60b8245%7Cd7811cdeecef496c8f91a1786241b99c%7C1%7C0%7C637758575012377269%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=4KrNhfLma5s8JpKS2aDysXe6JG2pNXmhn4kbjpS4IXw%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<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%7Cf7a035a7ca3a4680bd6d08d9c60b8245%7Cd7811cdeecef496c8f91a1786241b99c%7C1%7C0%7C637758575012377269%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=SWK9lxJwrk0ZlCrpq5JT6jxAKJ58fnp57Gxk21Lel3M%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<mailto: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<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%7Cf7a035a7ca3a4680bd6d08d9c60b8245%7Cd7811cdeecef496c8f91a1786241b99c%7C1%7C0%7C637758575012377269%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=GjEPA9otJrNCDaQdWlXmBeJj%2FTs2JXAZrw2VH66W6do%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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>>
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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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