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

[Xiaowen Chen]

Hi Shepherd,

I updated epihet in my github, then, I perform the following code:
git clone https://github.com/TheJacksonLaboratory/epihet.git
cd epihet
git remote add upstream git using git.bioconductor.org:packages/epihet.git
git remote -v

git fetch –all

Fetching origin
Fetching upstream
The authenticity of host 'git.bioconductor.org (34.192.48.227)' can't be established.
RSA key fingerprint is 8b:f5:32:b4:a1:bb:94:d2:a3:8c:1a:35:90:98:f6:4e.
Are you sure you want to continue connecting (yes/no)? yes
Warning: Permanently added 'git.bioconductor.org,34.192.48.227' (RSA) to the list of known hosts.
Permission denied (publickey).
fatal: The remote end hung up unexpectedly
error: Could not fetch upstream

I got the above error, could you give me some suggestion, I am not familiar git, I will appreciate it.

Thank you.
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/

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://github.com/%3cYour> github> .git (fetch)
origin https://github.com/<Your<https://github.com/%3cYour> 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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