[Bioc-devel] Bioconductor package tidybulk

[Shepherd, Lori]

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<mailto: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<mailto: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<mailto: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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