there is a lag between when the build report is published and when the web site
is updated. There is also a lag introduced by the content delivery network --
the landing pages are cached at potentially many locations (your computer, your
institution, the AWS cloudfront node). The lag can accumulate to several hours.
The most reliable source of information is the build report.
Martin
On 6/8/20, 1:17 AM, "Bioc-devel on behalf of stefano"
<bioc-devel-boun...@r-project.org on behalf of mangiolastef...@gmail.com> wrote:
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 <mangiolastef...@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.sheph...@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 g...@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 g...@git.bioconductor.org:packages/tidybulk.git (fetch)
>> upstream g...@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 <mangiolastef...@gmail.com>
>> *Sent:* Thursday, June 4, 2020 12:56 AM
>> *To:* Shepherd, Lori <lori.sheph...@roswellpark.org>
>> *Cc:* bioc-devel@r-project.org <bioc-devel@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 g...@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.sheph...@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 <mangiolastef...@gmail.com>
>> *Sent:* Wednesday, June 3, 2020 4:29 AM
>> *To:* Shepherd, Lori <lori.sheph...@roswellpark.org>;
>> bioc-devel@r-project.org <bioc-devel@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 <
>> mangiolastef...@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.sheph...@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@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]]
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
