[Bioc-devel] Bioconductor package tidybulk

Mon Jun 8 07:17:16 CEST 2020

Hello Lori and All,

I confirm that the bioconductor page for a package (e.g.,
https://www.bioconductor.org/packages/release/bioc/html/tidybulk.html ) has
a bug in practice. Namely that even though the icon build is green

https://wehieduau-my.sharepoint.com/:i:/g/personal/mangiola_s_wehi_edu_au/EbdbpGqJ8zZKhYjE3mJq8CsB6viFK6Ci6AoAQRzcD8hDbQ?e=lub86A

the actual build (e.g.,
http://bioconductor.org/checkResults/release/bioc-LATEST/tidybulk/) can be
failing.

If this is wanted, or tolerated, it is very confusing for developers (and
users) because communicate false confidence and leads to unwanted
neglection (as happened to me) .

Best wishes.

*Stefano *

Stefano Mangiola | Postdoctoral fellow

Papenfuss Laboratory

The Walter Eliza Hall Institute of Medical Research

+61 (0)466452544

Il giorno sab 6 giu 2020 alle ore 11:08 stefano <mangiolastefano using gmail.com>
ha scritto:

> 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
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