[Bioc-devel] [EXTERNAL]Re: Update R package I developed which has been released by bioconductor
Hi Shepherd, I tried to activate my account on https://git.bioconductor.org/BiocCredentials/account_activation/ Xiaowen.chen at jax.org<mailto:Xiaowen.chen at jax.org> which is shown in description file, but it told me: xiaowen.chen at jax.org<mailto:xiaowen.chen at jax.org> is not associated with a maintainer of a Bioconductor package. Please check the spelling or contact bioc-devel at r-project.org<mailto:bioc-devel at 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 at RoswellPark.org> Date: Friday, September 25, 2020 at 7:33 AM To: Xiaowen Chen <Xiaowen.Chen at jax.org>, "bioc-devel at r-project.org" <bioc-devel at 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 at jax.org>
Sent: Thursday, September 24, 2020 10:04 PM
To: Shepherd, Lori <Lori.Shepherd at RoswellPark.org>; bioc-devel at r-project.org <bioc-devel at r-project.org>
Subject: Re: [EXTERNAL]Re: Update R package I developed which has been released by bioconductor
Sent: Thursday, September 24, 2020 10:04 PM
To: Shepherd, Lori <Lori.Shepherd at RoswellPark.org>; bioc-devel at r-project.org <bioc-devel at 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 at git.bioconductor.org:packages/epihet.git (fetch) upstream git at git.bioconductor.org:packages/epihet.git (push) Is it right? Best, Xiaowen From: "Shepherd, Lori" <Lori.Shepherd at RoswellPark.org> Date: Monday, September 21, 2020 at 9:22 AM To: Xiaowen Chen <Xiaowen.Chen at jax.org>, "bioc-devel at r-project.org" <bioc-devel at 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 at git.bioconductor.org:packages/epihet (fetch) upstream git at 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 at r-project.org> on behalf of Xiaowen Chen <Xiaowen.Chen at jax.org> Sent: Monday, September 21, 2020 8:57 AM To: bioc-devel at r-project.org <bioc-devel at 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. 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