[Bioc-devel] Bioconductor package tidybulk

Sat Jun 6 03:08:36 CEST 2020

Thanks Lori,

your email finally made me understand the relationship between my repo and
Bioc repo. I have to admit that I was not familiar of remote vs. upstream.

Now, I have pushed everything to RELEASE_3_11. But the tests did not
trigger.

I will push to develop as well early next week.

Best wishes.

*Stefano *

Stefano Mangiola | Postdoctoral fellow

Papenfuss Laboratory

The Walter Eliza Hall Institute of Medical Research

+61 (0)466452544

Il giorno gio 4 giu 2020 alle ore 23:11 Shepherd, Lori <
Lori.Shepherd using roswellpark.org> ha scritto:

>
> 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> 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>
> *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
>
> 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.
>
>
> 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.
>
>
> 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.

	[[alternative HTML version deleted]]