[Bioc-devel] [EXTERNAL]Re: Update R package I developed which has been released by bioconductor

Fri Sep 25 14:12:32 CEST 2020

Hi Shepherd,

I tried to activate my account on https://git.bioconductor.org/BiocCredentials/account_activation/

Xiaowen.chen using jax.org<mailto:Xiaowen.chen using jax.org> which is shown in description file, but it told me:
xiaowen.chen using jax.org<mailto:xiaowen.chen using jax.org> is not associated with a maintainer of a Bioconductor package. Please check the spelling or contact bioc-devel using r-project.org<mailto:bioc-devel using r-project.org> for help.
 This is my epihet link: https://bioconductor.riken.jp/packages/3.9/bioc/html/epihet.html
Could you help me?
Best,
Xiaowen

From: "Shepherd, Lori" <Lori.Shepherd using RoswellPark.org>
Date: Friday, September 25, 2020 at 7:33 AM
To: Xiaowen Chen <Xiaowen.Chen using jax.org>, "bioc-devel using r-project.org" <bioc-devel using r-project.org>
Subject: Re: [EXTERNAL]Re: Update R package I developed which has been released by bioconductor

The remote set up you have is correct.  Based on your previous email and your new email to bioc-devel it looks like the issue is your access credentials/public key  and activating your git credentials account so you can manage keys.

Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Xiaowen Chen <Xiaowen.Chen using jax.org>
Sent: Thursday, September 24, 2020 10:04 PM
To: Shepherd, Lori <Lori.Shepherd using RoswellPark.org>; bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: Re: [EXTERNAL]Re: Update R package I developed which has been released by bioconductor

By the way, when I performed “git remote -v”

It is different with yours, I have a “.git” for upstream

origin     https://github.com/TheJacksonLaboratory/epihet.git (fetch)

origin     https://github.com/TheJacksonLaboratory/epihet.git (push)

upstream             git using git.bioconductor.org:packages/epihet.git (fetch)

upstream             git using git.bioconductor.org:packages/epihet.git (push)

Is it right?

Best,

Xiaowen

From: "Shepherd, Lori" <Lori.Shepherd using RoswellPark.org>
Date: Monday, September 21, 2020 at 9:22 AM
To: Xiaowen Chen <Xiaowen.Chen using jax.org>, "bioc-devel using r-project.org" <bioc-devel using r-project.org>
Subject: [EXTERNAL]Re: Update R package I developed which has been released by bioconductor

Bioconductor would not have your package on github.  Bioconductor has your repository in a git server.   If you already have a clone of your github repository you could follow the instructions here to add the remote to the Bioconductor repository you referenced here:

http://bioconductor.org/developers/how-to/git/sync-existing-repositories/<http://secure-web.cisco.com/1CGgZFviZNHf_PzBZoDIbYfrWRtCAwE3cXN_Br4oaRqMG09TfgkuIPaaxMorCSWOA2I-xG9LPFz8HvmW0DJCUsryRqjDpMlCCP8YGR-HE6UHUyiBMtcTmAA0Hv_au5qFFBiqwEtqSc9J3USTWIxrc2P3gDVByHH5nd1KeU-vuxvjj0iZWdcn6vjPhFCKcPkoYhIm8P5XMBNhJ9DFKM75lukyg2L4We-JZRzv--Rty7SvM78FRQOJ_2eTDHZeFm35Jr4nNl9tWOsEAUQNqBYKSxN4FmxewdWNw66l2EV-6qsKNUzbO1QV8_cEUZTvco2jt/http%3A%2F%2Fbioconductor.org%2Fdevelopers%2Fhow-to%2Fgit%2Fsync-existing-repositories%2F>

so :

git clone  <Your github repo>

cd epihet

<follow the instructions on the link above>

Make sure you do the

git fetch --all

git pull upstream master before making any changes!! This will make sure you get the release version bumps the core team performed and that everything is up-to-date with our version of your repository at git.bioconductor.org

Once you add the remote upstream if you do git remote -v

origin should point to your github

upstream should point to Bioconductor

It would be something similar to

origin https://github.com/<Your<https://secure-web.cisco.com/1jto4PqGAETGWWrZg1lJy8YTYiLxiUl6gMitOiLT-D9gFgHHJkw_50iAKfQD_Y8E-yvcvsQstFNjcCTuG0KbQi7vAxa3T_mSjpQJyFClUmFsBZrjmkvqRRxT7EXwChsNl-Hey6xDhuuoav2gXJqN8ogSDyK5oa3ZuPgiYMyctBxAd8NlrTcgj9CztmC__ziIZOaq4GKOHK8zzkngrqfKqbd9UqMtEVhpy93WVveVYXbzNZT72inuxFJSEAfyaD_pGEreCH1Ve-6JSCfxspTiqV9518XeNfXDIYzL_wVd_qG3nYj9_Xy0Kiop6kFuVXh5-/https%3A%2F%2Fgithub.com%2F%253cYour> github> .git (fetch)

origin https://github.com/<Your<https://secure-web.cisco.com/1jto4PqGAETGWWrZg1lJy8YTYiLxiUl6gMitOiLT-D9gFgHHJkw_50iAKfQD_Y8E-yvcvsQstFNjcCTuG0KbQi7vAxa3T_mSjpQJyFClUmFsBZrjmkvqRRxT7EXwChsNl-Hey6xDhuuoav2gXJqN8ogSDyK5oa3ZuPgiYMyctBxAd8NlrTcgj9CztmC__ziIZOaq4GKOHK8zzkngrqfKqbd9UqMtEVhpy93WVveVYXbzNZT72inuxFJSEAfyaD_pGEreCH1Ve-6JSCfxspTiqV9518XeNfXDIYzL_wVd_qG3nYj9_Xy0Kiop6kFuVXh5-/https%3A%2F%2Fgithub.com%2F%253cYour> github>.git (push)

upstream git using git.bioconductor.org:packages/epihet (fetch)

upstream git using git.bioconductor.org:packages/epihet (push)

So when you push changes:

git push origin master

would update YOUR github

it is saying git push  to the origin which is your github on the master branch

To update on Bioconductor

git push upstream master

it is saying git push changes to the upstream with is the bioconductor remote master branch (devel)

Make sure the version number has a version bump!  Our version is at 1.5.0  so you would have to bump the z of version x.y.z for it to register on Bioconductor (>=  1.5.1  )

Hope that helps clarify.

Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________

From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Xiaowen Chen <Xiaowen.Chen using jax.org>
Sent: Monday, September 21, 2020 8:57 AM
To: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: [Bioc-devel] Update R package I developed which has been released by bioconductor

Hi,
I submit R package called epihet on 2018. It has been accepted and released on Bioconductor.
Recently, we received the reviewers’ comments about the corresponding paper for epihet, and the reviewer need us to add more parameters for some function in epihet,
Could you tell me what I should do step-by-step? Now I know the link

  1.  http://secure-web.cisco.com/1-EVvVLIafjMbq01E8DqEQNgmvkKvvnjD-0pOAg6fnFQJZO7UJhpm74hsFevQdnOceH8Ueh2BWTT9kb9bsdL13IqIS93SOktOTaRvzl88vZQIjyKpVvpYcasFBguMZ539EF4nnf-yJhgY9ZqzCEecd6Lt5PcT0r6hY6iwYo-kRFbGTZgQvUYbiv4RVLCB0aMNRwNiL_faHaysCM-N9aMnkF0QCtDVuYHDOpwzG0F5eCLtvMhWpKTH29P3I5RfQgzRralE_Wz3O-tYENZrRrhyzlXMEbSEmVj6BtcGZ5p0YdkUaFJ_5NswJT984xe0R4_R/http%3A%2F%2Fbioconductor.org%2Fdevelopers%2Fhow-to%2Fgit%2Fsync-existing-repositories%2F for sync an existing GitHub repository with Bioconductor
  2.  http://secure-web.cisco.com/1a15GjCpVQyP3eF8WecbERPx8u0-Q3oUVwuRg9flwlizP3Dc6jfSdhF4CRMxd0I4M7S6UAfWCIbVnl67rKj6PsgIKMl5dppsGvqDKq8rf66Cm3qOq2JthrZCWEmdK4xZxV60M5gelNAIlZgVx1Q4HRDN_N4xilgDKIOy5WaMqWYc-57D0HIplyKyzL7xcmCZRnrdmYTfuxIAtS9KhxTHXcp1dfY6CZmW00wMdYPUWfUCkFjSe4_DancgDyMQkmB6EZ4S-PO5qKEdtIAkAEscewyygalAfrQEpiFigAz2iRvFjnDKvTOw5mBH4gvd0eGkb/http%3A%2F%2Fbioconductor.org%2Fdevelopers%2Fhow-to%2Fgit%2Fbug-fix-in-release-and-devel%2F for fix bugs in devel and release
but I still not sure which github repository I need to git clone on my local machine, my own github or Bioconductor github, but I did not found my package “epihet” on Bioconductor github

Thank you.
Best,
Xiaowen

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