[Bioc-devel] Bioconductor package tidybulk

Thu Jun 4 06:56:33 CEST 2020

Thanks Lori,

I have to questions

1)
I got versioning error

```

rstudio-1 267 % git push upstream master
Counting objects: 372, done.
Delta compression using up to 32 threads.
Compressing objects: 100% (276/276), done.
Writing objects: 100% (290/290), 1.13 MiB | 0 bytes/s, done.
Total 290 (delta 208), reused 21 (delta 13)
remote: Resolving deltas: 100% (208/208), completed with 41 local objects.
*remote: Error: Illegal version bump from '1.1.0' to '1.2.1'. Check *
remote: http://bioconductor.org/developers/how-to/version-numbering/
remote: for details
To git using git.bioconductor.org:packages/tidybulk.git

```

Even reading the guide
http://bioconductor.org/developers/how-to/version-numbering/ I don't
understand what applies to my case

2) I still don't know what is the best way to manage github development
with Bioconductor development.

I have my Master branch and I am pushing it to Bioconductor. Can I have a
RELEASE branch pushed to Bioconductor rather than my master branch?

guide: "Repeat for the release branch, replacing master with the name of
the release branch, e.g., RELEASE_3_6."

Thanks.

Best wishes.

*Stefano *

Stefano Mangiola | Postdoctoral fellow

Papenfuss Laboratory

The Walter Eliza Hall Institute of Medical Research

+61 (0)466452544

Il giorno mer 3 giu 2020 alle ore 23:36 Shepherd, Lori <
Lori.Shepherd using roswellpark.org> ha scritto:

> It will not be tested before integration.  We assume that all maintainers
> and R CMD build and R CMD check before submitting changes to Bioconductor.
>
> You will need to have activated your git credentials account
>
> https://git.bioconductor.org/BiocCredentials/login/?next=/BiocCredentials/
>
> And follow the instructions for pushing to git.bioconductor.org.
> We provide many help instruction files for different scenarios
>
> http://bioconductor.org/developers/how-to/git/
>
>
> You will most notably be interested in
> Syncing to Bioconductor
> http://bioconductor.org/developers/how-to/git/sync-existing-repositories/
>
> and pushing fixes to release and devel
> http://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/
>
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Comprehensive Cancer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
> ------------------------------
> *From:* stefano <mangiolastefano using gmail.com>
> *Sent:* Wednesday, June 3, 2020 4:29 AM
> *To:* Shepherd, Lori <Lori.Shepherd using RoswellPark.org>;
> bioc-devel using r-project.org <bioc-devel using r-project.org>
> *Subject:* Re: Bioconductor package tidybulk
>
> Hello Again,
>
> I would be happy to submit the github master with the patch tonight if you
> could please confirm the commit command. Will it be tested before
> integration I assume.
>
> Thanks a lot!
>
> Best wishes.
>
> *Stefano *
>
>
>
> Stefano Mangiola | Postdoctoral fellow
>
> Papenfuss Laboratory
>
> The Walter Eliza Hall Institute of Medical Research
>
> +61 (0)466452544
>
>
> Il giorno mer 3 giu 2020 alle ore 12:26 stefano <mangiolastefano using gmail.com>
> ha scritto:
>
> Thanks Lori, (it seems outlook lost my sent email)
>
>
>
> sorry I missed this. It's so strange, few days ago I checked at
>
>
> https://www.bioconductor.org/packages/devel/bioc/html/tidybulk.html
> <https://secure-web.cisco.com/1ymalO2Wo2gRPT4USwKYJChnovSH3sx87LQTVbhEAL5rIc3rN6fxBVq0xvtPe8K_Q-R_eFRNkhIlQj7WO0ojRaWF_pEyWlhdIOd2PMRLmE2OPNqgY5f94zo8UYWUGdcvlZcVx8reWZ3HqP5ZigV5z6s1O1vpAhOg7Ilz6E1U3-x5Ew-CEeVKmnYZe96PicWrzG2pfFGcttYa35E5pwKrrGI-dm5Sy6FKZhrPJtO-Qm65EpKlgjJg-S1H0Dng6El9eZl79ifySj3rIrEtYwcVvsRCgOGmn5RqrxF4_1vKVJl7MF59rIRIHqt-OR9BXO6Ol7hNnQze5_Kl_SbkOEyd9h_FG7hn_MIzYBsitEyDD5-8/https%3A%2F%2Fwww.bioconductor.org%2Fpackages%2Fdevel%2Fbioc%2Fhtml%2Ftidybulk.html>
>
>
> and the build was OK for devel and stable versions.
>
>
> I have done the fix
>
>
> commit d1fe5beb290765181e0ce377b890f453c62ea9da
>
>
> Should I (?)
>
>
> - integrate the commit to the tidybulk version present in Bioconductor,
> and push
>
> - or push the update github repo
>
>
> Could you point me to the resource tat states how to push to Bioconductor,
> so I'm sure I am doing the right thing.
>
>
> Thanks alot.
>
>
> Best wishes.
>
> *Stefano *
>
>
>
> Stefano Mangiola | Postdoctoral fellow
>
> Papenfuss Laboratory
>
> The Walter Eliza Hall Institute of Medical Research
>
> +61 (0)466452544
>
>
> Il giorno mer 3 giu 2020 alle ore 07:10 Shepherd, Lori <
> Lori.Shepherd using roswellpark.org> ha scritto:
>
> Hello Package Maintainer,
>
> The Bioconductor Team would like to notify you that your package is
> currently
> failing on release and devel versions of Bioconductor and has been for an
> extended period of time.  This is very problematic.  Please fix your
> package to
> R CMD build and R CMD check cleanly immediately to avoid deprecation of
> your
> package. If you are having trouble or have any further questions please
> reach
> out to the developers mailing list at bioc-devel using r-project.org
>
>
> We appreciate your immediate attention to this matter.
>
> Cheers
>
> http://bioconductor.org/checkResults/devel/bioc-LATEST/tidybulk
> <http://secure-web.cisco.com/1V0Xuq_KL0x1Cl4QqzHrj1dnBRaQhCCuV-22PXesIk07DaPPjoJ3QsrSPROh_5cXbYpawIN5i2Nq1BZR_hLHXPuM6pjQ-3eMVQGnIfUDaGyUaM2r0OKlVcRHQal8uBYNnIvQH6S2oehrbakBF8VT50ga-chmesQYDXRVuPo_IWNS6IIR3LBhvBnY1hv5_raI9CsjS9fUpU-G09_CAyRyUA17JrLjrtMAT4Bxi5T0NN53kKg2ZP4Unsqwtr5Oix4WaXxRCKrMa0s77HeePZYvUAYnkfUYZCiYXuVsqmRytlG92KumBHz-0P1es_zBp5JVmqn-Y3mjMBOwl7Vy8Lx1o8anxo8xN9qChrHFrl14SjZQ/http%3A%2F%2Fbioconductor.org%2FcheckResults%2Fdevel%2Fbioc-LATEST%2Ftidybulk>
> http://bioconductor.org/checkResults/release/bioc-LATEST/tidybulk
> <http://secure-web.cisco.com/1gjLzb1cWpFF_sHsM57h5yIYvuiIuFDLZmakncmleiFa_KJWoTiDpmLs9wxxenQRe9bjnc5MCunwT6ishis6WIailFEBNiwNXyJWEXo9_I4MXs7HnnVHP8L-aUJI9D52getJRFvo3Y1oau4z0D0sMu_33XBgwAkFIcpDb8aleVdkalFB6T0bdquwBcfn_pO0zBXW8UgXsoFB3_RvbY4sgsDnymfSGqVXlwELCaQ9euMvV9waafBekDjsrAOD5H7L_t2wd91GpDyI8LNZhIFPO1vmUtCO5BkFrYxJvEEoLmqNSftO5yyQ2UqMuB8OQeacnKOLGwd0V-6_USxeGmvqSxVi2BDpIV7ukHTLkFTScrn4/http%3A%2F%2Fbioconductor.org%2FcheckResults%2Frelease%2Fbioc-LATEST%2Ftidybulk>
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Comprehensive Cancer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
>
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