[Bioc-devel] Bioconductor package tidybulk

Thu Jun 4 15:10:58 CEST 2020

The master branch is the development branch (Bioc 3.12) .  The version  of  x.y.z   The y is always odd in devel  and even in release.  This is the very first section on the page you referenced.  http://bioconductor.org/developers/how-to/version-numbering/

We do not jump full y versions in the middle of a release.

The current RELEASE_3_11  version is  1.0.0  =  the appropriate version bump on this branch is  1.0.1

The current master version is 1.1.0  = the appropriate version bump on this branch is  1.1.1

If you are unfamiliar with git and github branches I encourage you to read more documentation about it.  There are many helpful tutorials.
You can have as many branches on your local github repository as you like. We recommend creating unique branches for bioconductor releases to mimic our branch structure.   In general, and to make it less confusing we would highly recommend using the master branch as the development branch and link that to the master (development version) of Bioconductor.   This would be consistent and then you can following the guides and tutorials listed on the Bioconductor help pages

http://bioconductor.org/developers/how-to/git/

The release branch is designed to always be a stable branch and should only be updated for bug corrections.
The master branch should be for development and new features.

We will assume you ran the following to set up your remotes as recommended:
git remote add upstream git using git.bioconductor.org:packages/tidybulk.git

if you do
git remote -v

you should see something similar:
origin  <link to your github> (fetch)
origin  <link to your github> (push)
upstream git using git.bioconductor.org:packages/tidybulk.git (fetch)
upstream git using git.bioconductor.org:packages/tidybulk.git (push)

To create and work on a release branch:

git fetch --all
# this gets all branches from all remotes

# The following would only need to be run once EVER!
git checkout -b RELEASE_3_11  upstream/RELEASE_3_11

# this says checkout  a branch (-b)  call it RELEASE_3_11  and have it copied/link to the code at  upstream/RELEASE_3_11 (the #bioconductor upstream remote branch of RELEASE_3_11)

After it is created, to switch to this branch on a daily basis you can simply:
git checkout RELEASE_3_11

git pull upstream RELEASE_3_11
# pulls changes from the upstream RELEASE_3_11 remote

# The following would only need to be run once EVER!   It creates a branch on your local github called RELEASE_3_11
git push -u origin RELEASE_3_11

Make your code changes to fix bugs! Make sure to do a valid version bump by bumping the  z  of version  x.y.z

git add <files>
git commit    # give an informative commit message

git push upstream RELEASE_3_11
# This should push to the Bioconductor git repository

git push origin RELEASE_3_11
# This should push to your github local git repository

git checkout master
# Switch back to your master branch for development and code changes

If you are ever confused on what branch you are on you can do
git branch

To work on the devel master branch the commands would be similar to above but using master

git pull upstream master  # pulls from git bioconductor
git pull origin master        # pull from your individual github

# make changes, commit changes

git push upstream master  # pushes to git Bioconductor
git push origin master   # push to your github

Hopefully that helped clarified and will get you started.

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: Thursday, June 4, 2020 12:56 AM
To: Shepherd, Lori <Lori.Shepherd using RoswellPark.org>
Cc: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: Re: Bioconductor package tidybulk

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/<http://secure-web.cisco.com/1Juo69PrrnIOXU2DlRv55eEvQE69YG8gNnojLbxZZWpn2-BCpwQ95EvShTW84fzr36gEkai208agWd63Ju9NfDXE-J9WHITwNW8oj6a0nxd1bS_UtLog1j_kotLO3TRPxw6votAQ8BdaCk4PzIaCZRX2wTPTRQsHNIV1_U4F47Y3w5QyE-kq7njCZrhtOzxb6HxIn6mtY-Xgj7a3Wkas_WsiIDmeKI8MdDFgePj_CwYe7BMLtq680xbPHpzYD-KvS32jkv_R8yL5Bqf2xd1lUZxeJU7rCj4PTKVa0Q9JgSdl3ax7Ozze9-LxNvuOsmqKWWGorQqVctJQPHiJjwDlmPjmeCsjgtgODdtBWqLJ73s4/http%3A%2F%2Fbioconductor.org%2Fdevelopers%2Fhow-to%2Fversion-numbering%2F>
remote: for details
To git using git.bioconductor.org:packages/tidybulk.git

```

Even reading the guide http://bioconductor.org/developers/how-to/version-numbering/<http://secure-web.cisco.com/1Juo69PrrnIOXU2DlRv55eEvQE69YG8gNnojLbxZZWpn2-BCpwQ95EvShTW84fzr36gEkai208agWd63Ju9NfDXE-J9WHITwNW8oj6a0nxd1bS_UtLog1j_kotLO3TRPxw6votAQ8BdaCk4PzIaCZRX2wTPTRQsHNIV1_U4F47Y3w5QyE-kq7njCZrhtOzxb6HxIn6mtY-Xgj7a3Wkas_WsiIDmeKI8MdDFgePj_CwYe7BMLtq680xbPHpzYD-KvS32jkv_R8yL5Bqf2xd1lUZxeJU7rCj4PTKVa0Q9JgSdl3ax7Ozze9-LxNvuOsmqKWWGorQqVctJQPHiJjwDlmPjmeCsjgtgODdtBWqLJ73s4/http%3A%2F%2Fbioconductor.org%2Fdevelopers%2Fhow-to%2Fversion-numbering%2F> 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<mailto: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/<https://secure-web.cisco.com/1Aev5P9rDulkX5gOO8VsMROu0hqZcaU8fT3GP3AsyJYVM9ZzDQvHlsVkbzeE5uPiKDW76VZwZ3dFyNb8zGzGedrlNvKLuUclm-kcov6rBNxdEZC-UhloV7M-ybiYfSTo_9W9bVXIABeFOmC9RDlfjHPMBzpGAXgiSnFf5l9K5oZD2ttL2bFFzyPVpHc98pUcmuZnen8jgx7jpHxlJFEawIVU-cudLdHJRrrNkdaugeByvKC8QmZVUl5yXhLW4u6W1lt8pI3lSWOkBrmRgF7WmwU8fYTV4Bt9KeQha0JL0Ib9xgNh7Z8_Fp1tahQkwEDcvWHuhHTGYdGdQEeOAX9EAsg/https%3A%2F%2Fgit.bioconductor.org%2FBiocCredentials%2Flogin%2F%3Fnext%3D%2FBiocCredentials%2F>

And follow the instructions for pushing to git.bioconductor.org<http://secure-web.cisco.com/1tu10p-DtLwvt_Da5m6yfRWyEgCLKIttPMfLoP3QlI066eirYetcxcfKZxywtszpwBOI-HXVBFYGxT5HvijqFtWL7O7_Zjr-XYb9wiSmV8IzxJM4zQlSf_TZutg6lzUjtNw6qzutYzLhPuDrtXAWn5l9LzB3a6zQM4fOq2p5zz9-uY9qHeNvD9xBNMcBK8hjshH4JG3jV5BsTwRLsA0-lpp0CThGV35Cx7-aa55-G0DmN5onTbNlXqsO86CxJG0SEZ2-L9xGF-VVBgNI6g9ian3TxNbcjVdafZO9bacD0DGVsh_is1U_C_rrJLcCwum_BVFADYTVu1TSeEpqlnhx5mw/http%3A%2F%2Fgit.bioconductor.org>.
We provide many help instruction files for different scenarios

http://bioconductor.org/developers/how-to/git/<http://secure-web.cisco.com/1H0LIZjlbeI4hZ6lwLBpmwzeK1pJm_lvmM4EwXQRDqho3xCDLinHlAxc07U3mNV7suKrnr_1AfmGquSG6e-yn_XbbpGOECsw7mPV-meDnIfDmwkfm2CwS_i3IZIAkA6cxyGKdej44dWdQjbkKWg2JGtWv8loY6wj63Lbijzig-aulyMswz9PUgRYM0tM8U9UHwyValzmseILpTPkTCSTyJu7PBZGdFFxaicBJgFmBtZoyFQCFf7oXPizmmSyKvEh0MwgXgvznurtQXe5rMBDkwqySlrRTkXrbjuoxB9WPl-u8pWRhEjCve7ik5tNFoQacKKwNcxMCZ2aw7ySrEdkLFSZu41YG_a4r9FRfsL-DcJY/http%3A%2F%2Fbioconductor.org%2Fdevelopers%2Fhow-to%2Fgit%2F>

You will most notably be interested in
Syncing to Bioconductor
http://bioconductor.org/developers/how-to/git/sync-existing-repositories/<http://secure-web.cisco.com/1KZeBzEmS1uWIu3n6-dmHGrHtnY7o7_9uZjIzXpYceEvUgdbfHYiEnDuPGG29xPpe3Cq38dl6VxMCZHvMy2vz4QI7KqYKeBJIjAPcCXoW48yqNwZNwtT46CGd18cIxep7bqfEYsXVJYa_v21zdF6vq_AoEMdFolfkBi1RzkvRBSBu1mtnaSNxb2p266dTQXvReetXZ888aOqIlJLHV7aOr21aPL-JbZkdc0pH5Pobr_whr4fdIqjMBSSHjJtLgIpkhBojlnXd2s8htweMWUdyIJvxAa6oLGHSeq5I8pFJ9VaYQfiwsMKmg9Og6zgNbnV6Qi3HaigpOvMDngGfpjcU6Tdv2Z_2RWPnbC0kU3GaXqM/http%3A%2F%2Fbioconductor.org%2Fdevelopers%2Fhow-to%2Fgit%2Fsync-existing-repositories%2F>

and pushing fixes to release and devel
http://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/<http://secure-web.cisco.com/11yyfZ49Z7npZG1IQtNUChMTmptQod64On2gbAqHzqYn1F1s9qvsOhhqenc0W0Yz_LFDKi7C2l4qBlnP8kH5NQxApFKOpNh4MXd_V6F4f9cFuXZnY7RY_H4l_Ui8Dkcs3hxkE8VlyCpQls-YMNdbres6dkRdxTAlFP2nnPOZR-C5AOEwXXFl8TIQsMCouGEI9NyhwARVEBhxbDS2zb0IbAQUV2JOoX8XQLURMsmSHh3bOqFPstQWvtl51bPts8OqEBi1Q1-vx1abhxEtXWhb_ZEQMGjq8aK62LeukCl_bnHMdd3OOVJjuv0ygZyn4wUK_Pwx5aGl7iMBLEt_FuEnhZazI5Tlf9slOoZNiVaGHuck/http%3A%2F%2Fbioconductor.org%2Fdevelopers%2Fhow-to%2Fgit%2Fbug-fix-in-release-and-devel%2F>

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<mailto: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<mailto:bioc-devel using r-project.org> <bioc-devel using r-project.org<mailto: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

This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.

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