Git Push -u Origin Master Permission Denied (Publickey) Fatal: Could Not Read From Remote Repository

Frequently asked questions

1. I can't access my package.

   You will need to log in to the BiocCredentials app. If yous take non logged in before, you must first actuate your account.

   There are two steps,

   1. If there is no SSH key registered, you lot must add one.

   2. If in that location is already an SSH key registered, cheque the packages y'all accept access to in the 'Profile' interface.

   Y'all can alternatively check if yous accept access to your package using the command line

                                 ssh -T git@git.bioconductor.org                          

   If you have access to your parcel, simply cannot git pull or push, delight check FAQ #13, #14, and #15.

2. I'm a programmer for Bioconductor, my package ExamplePackage is on the new server https://git.bioconductor.org. What do I do next?

   Have a expect at Maintain GitHub and Bioconductor repositories. This will give y'all the data needed.

   NOTE: This situation is for packages which were previously maintained on SVN and have never been accessed through GIT. It is not for newly accepted packages through Github.

3. I accept a GitHub repository already fix for my Bioconductor package at www.github.com/<developer>/<ExamplePackage> , how exercise I link my repository in GitHub and https://git.bioconductor.org ?

   Have a wait at New package workflow. Pace 2 gives you information on how to add the remote and link both GitHub and Bioconductor repositories.

4. I'm unable to push or merge my updates from my GitHub repository to my Bioconductor parcel on git@git.bioconductor.org, how exercise I get virtually this?

   If you are unable to button or merge to either your GitHub account or Bioconductor repository, it means y'all exercise not take the correct access rights. If you lot are a developer for Bioconductor, you volition need to submit your SSH public primal to the BiocCredentials app.

   You should also make sure to check that your public central is prepare correctly on GitHub. Follow Adding an SSH key to your GitHub account.

5. I'yard not certain how to fetch the updates from git.bioconductor.org with regards to my package, how do I practise this?

   Take a wait at Sync existing repositories. This will give you the information needed.

6. I'm just a parcel user, do I need to do any of this?

   As a packet user, you exercise not need any of these developer related documentation. Although, information technology is a proficient primer if yous want to be a contributor to Bioconductor.

   You can also open pull requests and issues on the Bioconductor packages y'all use, if they have a GitHub repository.

7. I'm new to git and GitHub, where should I learn?

   In that location are many resource where y'all can learn about git and GitHub.

   • git-and-github-learning-resource
   • git-scm
   • Guides

8. I'grand a Bioconductor package maintainer, but I don't have access to the Bioconductor server where my packages are beingness maintained. How practise I proceeds access?

   Please submit your SSH public key using the BiocCredentials app. Your key will be added to your our server and y'all will get read+ write admission to your package.

   All developers of Bioconductor packages are required to do this, if they don't already have access. Please identify which packages you need read/write access to in the electronic mail.

9. What is the relationship betwixt the origin and upstream remote?

   In git lingo origin is just the default name for a remote from which a repository was originally cloned. Information technology might as have been chosen by another proper noun. We recommend that origin exist fix to the developers GitHub repository.

   Similarly, upstream is the name for a remote which is hosted on the Bioconductor server.

   It is of import that all the changes/updates you have on your origin are equal to upstream, in other words, yous want these two remotes to be in sync.

   Follow Sync existing repositories for details on how to accomplish this.

   Image explaining GitHub and Bioconductor human relationship for a programmer

   

10. Can I take more than one upstream remote, if yeah, is this recommended?

    You lot tin can have as many remotes as you please. But you can have only one remote with the name upstream. Nosotros recommend having the remote origin prepare to GitHub, and upstream set to the Bioconductor git server to avoid confusion.

11. Mutual names used in the scenario'due south

    developer: This should be your GitHub username, east.g., mine is nturaga.

    BiocGenerics: This is being used as an example to demonstrate git commands.

    ExamplePackage: This is being used a place holder for a package name.

    SVN trunk and git principal branch are now the development branches.

12. I'm a Bioconductor developer only on the Bioconductor server. I exercise non have/want a GitHub account. What should I exercise?

    You exercise not take to get a Github account if you exercise not want one. Merely information technology is a really good idea, to maintain your package publicly and collaborate with the customs via the social coding features available in Github.

    We highlight this in Maintain a Bioconductor-but repository

13. I cannot button to my bundle. I get the fault,

                                  $ git push button origin master  fatal: remote error: FATAL: Westward whatsoever packages/myPackage nobody DENIED by fallthru  (or y'all mis-spelled the reponame)                          

    (y'all might have renamed the origin remote as upstream; substitute upstream for origin. Check your remote,

                                  $ git remote -v  origin  https://git.bioconductor.org/packages/myPackage.git (fetch)  origin  https://git.bioconductor.org/packages/myPackage.git (push)                          

    As a developer you lot should be using the SSH protocol, simply the origin remote is HTTPS. Apply

                                  git remote add together origin git@git.bioconductor.org:packages/myPackage                          

    to modify the remote to the SSH protocol. Note the : after the host proper name in the SSH protocol, rather than the / in the HTTPS protocol. Confirm that the remote has been updated correctly with git remote -5.

    If your remote is correct and you nonetheless see the message, so your SSH key is invalid. Meet the next FAQ.

14. Earlier sending a question to the Bioc-devel mailing listing about git, delight bank check the output of the following commands for correctness so that we tin aid yous better.

    • As a programmer bank check to make sure, y'all are using SSH every bit your access protocol. Bank check the output of git remote -v for consistency. Include this in your email to bioc-devel, if you are unsure. The remote should look similar,

                                            origin  git@git.bioconductor.org:packages/myPackage.git (fetch)   origin  git@git.bioconductor.org:packages/myPackage.git (push button)                                  

      or

                                            origin  git@github.com:<github username>/myPackage.git (fetch)   origin  git@github.com:<github username>/myPackage.git (push)   upstream  git@git.bioconductor.org:packages/myPackage.git (fetch)   upstream  git@git.bioconductor.org:packages/myPackage.git (push)                                  

    • Check if you have admission to the bioc-git server (git@git.bioconductor.org), by using ssh -T git@git.bioconductor.org. This will show you a list of packages with READ(R) and WRITE(W) permissions. Every bit a developer you should accept R W adjacent to your packet. This is based on the SSH public key you are using, the default for ssh authentication is id_rsa.

                                            R    	admin/..*   R    	packages/..*   R  	admin/manifest   R  	packages/ABAData   R  	packages/ABAEnrichment   R  	packages/ABSSeq   R W  	packages/ABarray   R  	packages/Top   R  	packages/ADaCGH2   R  	packages/AGDEX                                  

15. SSH primal not being recognized because of unlike proper name?

    If you have named your SSH public key differently from id_rsa as suggested by ssh-keygen, you may notice it useful to gear up a ~/.ssh/config file on your car. Merely make a ~/.ssh/config file if it does not be, and add,

                                  host git.bioconductor.org      HostName git.bioconductor.org      IdentityFile ~/.ssh/id_rsa_bioconductor      User git                          

    In this case, my private key is chosen id_rsa_bioconductor instead of id_rsa.

    You may detect information technology useful to bank check the BiocCredentials app to see what SSH primal you take registered.

16. SSH key asking for a password and I don't know it? How do I retrieve information technology?

    There are a few possibilities hither,

    • You have fix a password. The bioc-devel mailing list cannot help y'all with this. Y'all have to submit a new central on the BiocCredentials app.

    • The permissions on your SSH central are incorrect. Verify that the permissions on SSH IdentityFile are 400. SSH will reject, in a not conspicuously explicit style, SSH keys that are too readable. Information technology will merely wait like a credential rejection. The solution, in this case, is (if your SSH central for bioconductor is called id_rsa):

                                            chmod 400 ~/.ssh/id_rsa                                  

    • Yous accept the wrong remote fix, please check git remote -v to make certain the SSH access protocol is being used. Your bioc-git server remote, should be git@git.bioconductor.org:packages/myPackage.

17. Can I create and push new branches to my repository on git.bioconductor.org?

    No. Maintainers only accept admission to master and the current RELEASE_X_Y. New branches cannot exist created and pushed to the bioconductor server. We recommend maintainers have boosted branches on their Github repository if they are maintaining one.

18. How can I ready my duplicate commits issue and find the required documentation?

    The detailed documentation to resolve indistinguishable commits tin be plant at the link.

More questions?

If you take boosted questions which are not answered here already, please send an email to bioc-devel@bioconductor.org.

Helpful links:

Bioconductor source control overview.

Adding a new SSH key to your GitHub account

Create a pull request on GitHub

Create an issue on GitHub

Git and GitHub learning resource

git-scm manual

GitHub Guides

bennettgavis1947.blogspot.com

Source: https://bioconductor.org/developers/how-to/git/faq/

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