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

Wed Jan 5 14:33:17 CET 2022

Dear Lori,
thank you for your clarifying and my apologies for misunderstanding.

Best,

Emanuela
________________________________
Da: Kern, Lori <Lori.Shepherd using RoswellPark.org>
Inviato: mercoledì 5 gennaio 2022 13:41
A: Emanuela Iovino <emanuela.iovino using unibo.it>; bioc-devel using r-project.org <bioc-devel using r-project.org>; sperez using roswellpmarcel.ramoark.org <sperez using roswellpmarcel.ramoark.org>; Nitesh Turaga <nturaga.bioc using gmail.com>
Oggetto: Re: [Bioc-devel] I: EXTERNAL: R: release of new version of package

Bioconductor has two different active branches a release branch and a devel branch.  The changes pushed to master are for the devel (3.15) branch.
Which are reflected in the devel build report:
http://bioconductor.org/checkResults/3.15/bioc-LATEST/uncoverappLib/

In order for your changes to appear on the page you linked :
https://bioconductor.org/checkResults/3.14/bioc-LATEST/uncoverappLib/

You would need to make changes and push to the corresponding release branch.  In this case RELEASE_3_14
See:  http://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/

Also keep in mind we really encourage only updating the release branch to fix bugs and errors and not for new features.  New enhancements to packages should be on the devel branch.

Hope this helps clarify

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 Emanuela Iovino <emanuela.iovino using unibo.it>
Sent: Wednesday, January 5, 2022 7:36 AM
To: bioc-devel using r-project.org <bioc-devel using r-project.org>; sperez using roswellpmarcel.ramoark.org <sperez using roswellpmarcel.ramoark.org>; Nitesh Turaga <nturaga.bioc using gmail.com>
Subject: [Bioc-devel] I: EXTERNAL: R: release of new version of package

Dears
I'm sorry to bother you with this again,
I followed you suggestions to up-to-date the changes of my package (https://secure-web.cisco.com/1AYgDbNKiFob0Cd3xIGF1BOB6n6U9j9IKNwz7AqdU55OA7GZzFD_LwJze8oq73godqsOGMtN_JW-CBxRRHIOIPyB9j4fHNz4R5KmIzyCA9vno3nKQfKDVKX2jwWXznEkCjdOz8jfUNwBo9h6Q5nWKQDT2LR60Oye5xkzQNFk0ZWIUM8GIQUugiUujE7yJXODmYMYm0fZaWil2_gIeSM0JUmJLWpwWxiLT18ID7ibgXmkD829bG1Gv8E1AosUGdUXoVdmWTWYA-lgqdYYQaFD71NjjVQLNKFTppwC_XwRLHT_so2OzFSRqVJvwj6IUdY3T/https%3A%2F%2Fgithub.com%2FManuelaio%2FuncoverappLib) pushing them on master branch.
I’m looking on https://secure-web.cisco.com/1-e3XnkhxHDJAfhk7cASrEnvin3c6XcenJED5PRDX0p6NIWbcD8WSR7fTSWZzshhjrD5qW-m7kKtYOX3cyrzTHZ888o-CqVlszSSnQk6VwThlLdKrDBs9F7a4iqs6kfNUETP0GiePcv6K_risgchRc36cSGukrZXEV0ZF7xeUfGO3DGfv7LAVNKX1zAIwdpDPuJBRFw2OdHr4WOxQr6OwEi0QmYh9Gaift3wvygHsUJcaqP-Rcio4KOpibOzXF0IhSL33LwipNTANN5XM5IWxOKMgS7LDqouCICSuoTRciMgrE_o_HJd00A4iczZr6_c2/https%3A%2F%2Fbioconductor.org%2FcheckResults%2F3.14%2Fbioc-LATEST%2FuncoverappLib%2F and the last hash commit doesn't correspond with the most recent commit in my repo.
On my Github, the last commit is form 5 days ago meanwhile on Bioconductor link it is from Tue, 26 Oct 2021.
Now, when I try to do git push upstream master I receive  Everything up-to-date

I believe that I don’t’ have got correctly UpToDate Bioconductor git, as you can see on attached screenshot of my repo. Is there any way to check this?

Emanuela

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,

________________________________
Da: Bioc-devel <bioc-devel-bounces using r-project.org> per conto di Marcel Ramos <sperez using roswellpmarcel.ramoark.org>
Inviato: lunedì 20 dicembre 2021 20:02
A: bioc-devel using r-project.org <bioc-devel using r-project.org>
Oggetto: 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 onhttp://bioconductor.org/checkResults/release/bioc-LATEST/uncoverappLib/  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)http://secure-web.cisco.com/1xscKz6h0-j1GWk22d6LTvhErBQlH7fGkYedpMJ_72jGlOvVHoW9CK_wfzlfwCG3xhHBcDopWUtJ2gBAjseWFgxzCFYdpGG3K2OrJhQr9Fu2-Q_QJZaGqvw5br1UlONB7O9ZHZVRJWh0hlI1gavjUiwNMOfxmWgEtvRLK0s4WdP0karEHt4JAgGZOMK1MZoopFbdx9uDZ0sOQl72D9i1n-sqiEWRBSGJrnYj9Q8-b5KfL5ay9o0Zt0JQuZuq_UP6vh2XBPBSXXaaqaIHMmt7yaPhTpIbRs1nVZT2tm7_HgqHSpLVveaiU3Y6z3jnZoLz7/http%3A%2F%2Fbioconductor.org%2Fdevelopers%2Fhow-to%2Fgit%2Fsync-existing-repositories%2F
>
> (2)https://secure-web.cisco.com/1aYeLYgfjnE8ouw7cpIUjdV7dKbN3aQyp1ZP48CBvQqhEvBp9IzFEK7i47lfAJnLle-yYgd7qcOvVFh_NYqB-qf5VthnXmZojNucvj-sP1Cb6UsQQ7OEkB6XouZwzgZMt9HdO_qPB6mJ8GXWijnQ07VYWlW8TF8TySsNLZj7IlEiEFwpeInkHZQQALbp07ua2nGV0gVeVW8BIDcq9MoMXMoRIni79CsGlN1YalJw3omT6lEtKZlU-Jjj6gKDYcYeCXuy8kUcF8vkvA1o-8zRjXKzAVN4-HgVqdfEW927Uefc1isaXjgGKX1_mM9tCuC34/https%3A%2F%2Fbioconductor.org%2Fdevelopers%2Fhow-to%2Fgit%2Fpush-to-github-bioc%2F
>
> 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://secure-web.cisco.com/1nVGeYEh4u414YOl_3mUQ4oBz9nPVoFWS-WaHtfjNvetiX7_BPT5F1iL1tqkEbexjCdYmV9_imfuTaztCMFr_Nh4_EZtnVhfo_YLt-V0pAz_neRZEodDCbaiPqYGTfQ5hjtBhF1k8K4xDcHQe1IKgP-oFQFRSeWX0XvWIh-uvVIhru1sUkRKUgmAuSylJnofxt1ks-H8EmSSVcYOwBLiCCJVKiNjniTItQJShq9XnLi6TMNlNXQRhFFgWpYPqcY6tl5rdIbQsp2HEhTEvyu-o5qPv5Dpnepmys_YW7vYs7pV3FlZm4w65GpNPTdfLp4z3/https%3A%2F%2Fbioconductor.org%2Fdevelopers%2Fhow-to%2Fgit%2Fnew-package-workflow%2F
>> 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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