[Bioc-devel] EXTERNAL: Re: Cannot move 'xps' to GIT
Turaga, Nitesh
Nitesh.Turaga at RoswellPark.org
Fri Oct 13 20:12:15 CEST 2017
Hi,
Both your `origin` and `upstream` are set to the same location i.e git at git.bioconductor.org:packages/xps.
This is wrong. You want your origin to point to `git at github.com:cstrato/xps`
You can do this by following the commands,
`git remote set-url origin git at github.com:cstrato/xps.git`
`git push origin master`
All of this documentation is given in bioconductor.org/developers/how-to/git/.
Best,
Nitesh
> On Oct 13, 2017, at 2:07 PM, cstrato <cstrato at aon.at> wrote:
>
> Dear Martin,
>
> Following your advice
>
> https://bioconductor.org/developers/how-to/git/maintain-github-bioc/
>
> I did the following:
>
> $ cd xps
> $ git remote add upstream git at git.bioconductor.org:packages/xps.git
> $ git fetch upstream
> Enter passphrase for key '/Users/rabbitus/.ssh/id_rsa':
> From git.bioconductor.org:packages/xps
> * [new branch] RELEASE_2_10 -> upstream/RELEASE_2_10
> * [new branch] RELEASE_2_11 -> upstream/RELEASE_2_11
> * [new branch] RELEASE_2_12 -> upstream/RELEASE_2_12
> * [new branch] RELEASE_2_13 -> upstream/RELEASE_2_13
> * [new branch] RELEASE_2_14 -> upstream/RELEASE_2_14
> * [new branch] RELEASE_2_2 -> upstream/RELEASE_2_2
> * [new branch] RELEASE_2_3 -> upstream/RELEASE_2_3
> * [new branch] RELEASE_2_4 -> upstream/RELEASE_2_4
> * [new branch] RELEASE_2_5 -> upstream/RELEASE_2_5
> * [new branch] RELEASE_2_6 -> upstream/RELEASE_2_6
> * [new branch] RELEASE_2_7 -> upstream/RELEASE_2_7
> * [new branch] RELEASE_2_8 -> upstream/RELEASE_2_8
> * [new branch] RELEASE_2_9 -> upstream/RELEASE_2_9
> * [new branch] RELEASE_3_0 -> upstream/RELEASE_3_0
> * [new branch] RELEASE_3_1 -> upstream/RELEASE_3_1
> * [new branch] RELEASE_3_2 -> upstream/RELEASE_3_2
> * [new branch] RELEASE_3_3 -> upstream/RELEASE_3_3
> * [new branch] RELEASE_3_4 -> upstream/RELEASE_3_4
> * [new branch] RELEASE_3_5 -> upstream/RELEASE_3_5
> * [new branch] master -> upstream/master
> $ git fetch upstream
> Enter passphrase for key '/Users/rabbitus/.ssh/id_rsa':
> $ git merge upstream/master
> Already up-to-date.
> $ git push origin master
> Enter passphrase for key '/Users/rabbitus/.ssh/id_rsa':
> Everything up-to-date
> $ git remote -v
> origin git at git.bioconductor.org:packages/xps (fetch)
> origin git at git.bioconductor.org:packages/xps (push)
> upstream git at git.bioconductor.org:packages/xps.git (fetch)
> upstream git at git.bioconductor.org:packages/xps.git (push)
> $ git checkout master
> M DESCRIPTION
> M NEWS
> M configure.in
> Already on 'master'
> Your branch is up-to-date with 'origin/master'.
> $ git add -v DESCRIPTION
> add 'DESCRIPTION'
> $ git add -v NEWS
> add 'NEWS'
> $ git add -v configure.in
> add 'configure.in'
> $ git push origin master
> Enter passphrase for key '/Users/rabbitus/.ssh/id_rsa':
> Everything up-to-date
> $ git push upstream master
> Enter passphrase for key '/Users/rabbitus/.ssh/id_rsa':
> Everything up-to-date
>
>
> I hope that I could commit my changes and my development version on
>
> https://github.com/cstrato/xps
>
> will be updated to 'xps_1.37.2'
>
>
> (PS: my repository https://github.com/cstrato/xps is still empty)
>
> Thank you very much for your help.
> Best regards,
> Christian
>
>
> On 10/12/17 23:21, Martin Morgan wrote:
>> On 10/12/2017 04:13 PM, cstrato wrote:
>>> Dear Martin,
>>>
>>> Thank you for your informative reply.
>>>
>>> 1, My SSH public key that you mentioned is the correct one.
>>>
>>>
>>>
>>> 2, After following your advice and running
>>>
>>> ssh -v git at git.bioconductor.org
>>>
>>> I got:
>>>
>>> OpenSSH_7.4p1, LibreSSL 2.5.0
>>> debug1: Reading configuration data /etc/ssh/ssh_config
>>> debug1: Connecting to git.bioconductor.org [34.192.48.227] port 22.
>>> debug1: Connection established.
>>> debug1: identity file /Users/rabbitus/.ssh/id_rsa type 1
>>> debug1: key_load_public: No such file or directory
>>> ...
>>> debug1: Remote: PTY allocation disabled.
>>> PTY allocation request failed on channel 0
>>> hello c.stratowa, this is git at ip-172-30-0-33 running gitolite3 v3.6.6-6-g7c8f0ab on git 2.13.0
>>> ...
>>> bash: debug1:: command not found
>>>
>>>
>>>
>>> 3, Nevertheless, I could run:
>>>
>>> git clone git at git.bioconductor.org:packages/xps
>>>
>>> I got:
>>> Cloning into 'xps'...
>>> Enter passphrase for key '/Users/rabbitus/.ssh/id_rsa':
>>> remote: Counting objects: 2757, done.
>>> remote: Compressing objects: 100% (2741/2741), done.
>>> remote: Total 2757 (delta 2077), reused 0 (delta 0)
>>> Receiving objects: 100% (2757/2757), 5.62 MiB | 945.00 KiB/s, done.
>>> Resolving deltas: 100% (2077/2077), done.
>>> Checking connectivity... done.
>> From the Bioconductor perspective, I think you are 'good to go', and you could follow, e.g.,
>> http://bioconductor.org/developers/how-to/git/maintain-bioc-only/
>> to commit and push changes to the Bioconductor git repository. These changes would be incorporated into the nightly builds, etc., as before.
>>> 4, In 'https://github.com/settings/keys' I deleted the old SSH key and tried to add a new SSH key, where in 'Key' I copied once again my public 'id_rsa'. However, once again I received an email with the wrong key 'df:2d:78:4f:**'
>> This is the 'fingerprint' of the SSH public key, rather than the public key itself.
>>> I do not understand why my correct key is not accepted.
>>>
>>> According to 'https://caius.github.io/github_id/' my user id is:
>>> cstrato is github user #32616897
>>>
>>> My public key at 'https://github.com/cstrato.keys' is still empty.
>>>
>> I don't know the answer to this github question; maybe public keys are not displayed by default? At any rate it 'does not matter'; github allows you to clone via https + password, or via ssh; all you need is to be able to clone your newly created, empty github xps repository, which it seems from below that you can.
>> It sounds like, now that you have access to git.bioconductor.org, you could follow
>> https://bioconductor.org/developers/how-to/git/maintain-github-bioc/
>> Martin
>>>
>>> I am not sure what I need to do next?
>>>
>>> Thank you.
>>> Best regards,
>>> Christian
>>>
>>>
>>> On 10/12/17 19:40, Martin Morgan wrote:
>>>> On 10/08/2017 01:37 PM, cstrato wrote:
>>>>> Dear all,
>>>>>
>>>>> I wanted to update my package 'xps' and realized that I can no longer use 'svn commit'
>>>>>
>>>>> In order to use GIT I did the following:
>>>>>
>>>>>
>>>>> 1, I created a public key '~/.ssh/id_rsa.pub'
>>>>>
>>>>>
>>>>> 2, I did submit my 'SSH public key or github id to Bioconductor', using the 'git/svn transition: ssh keys' form.
>>>>>
>>>>> Here I entered my SVN user id, but it was not clear what my ID is.
>>>>> So I checked 'svn info' and used first my name 'c.stratowa' as SVN user id.
>>>>> Since I did not succeed I repeated the procedure and used the UUID as SVN user id.
>>>>>
>>>>> Is this correct, or how do I get my SVN user id?
>>>>>
>>>>>
>>>>> 3, I created a new GitHub repository:
>>>>>
>>>>> https://github.com/cstrato/xps
>>>>>
>>>>>
>>>>> 4, Then I tried to clone the empty repository from GitHub. Here is the result:
>>>>>
>>>>> iMac:GIT cstrato$ git clone https://github.com/cstrato/xps.git
>>>>> Cloning into 'xps'...
>>>>> warning: You appear to have cloned an empty repository.
>>>>> Checking connectivity... done.
>>>>> iMac:GIT cstrato$ git clone https://github.com/cstrato/xps.git
>>>>> fatal: destination path 'xps' already exists and is not an empty directory.
>>>>> iMac:GIT cstrato$ cd xps
>>>>> iMac:xps cstrato$ git remote add upstream git at git.bioconductor.org:packages/xps.git
>>>>> iMac:xps cstrato$ git fetch upstream
>>>>> Permission denied (publickey).
>>>>> fatal: Could not read from remote repository.
>>>>
>>>> there's a single public key associated with access to xps, ending with
>>>>
>>>> /m+bdjnFrDw5Fod8Sa9zDh2vXcICrNcxWGds2rbG3Q==
>>>>
>>>> that should correspond to one of the public keys in your ~/.ssh/ directory. If not, resubmit the form with You can try
>>>>
>>>> ssh -v git at git.bioconductor.org
>>>>
>>>> and try to diagnosis why this public key is not being matched; a possibility is FAQ #15 where git is choosing the wrong key
>>>>
>>>> https://bioconductor.org/developers/how-to/git/faq/
>>>>
>>>>>
>>>>> Please make sure you have the correct access rights
>>>>> and the repository exists.
>>>>>
>>>>>
>>>>> 5, I realized that I needed to add my public key to:
>>>>> https://github.com/settings/keys
>>>>>
>>>>> The email I got was:
>>>>> The following SSH key was added to your account:
>>>>> iMac
>>>>> df:2d:**:**:** etc
>>>>
>>>> no, that doesn't look like an ssh key, it looks like a MAC address.
>>>>
>>>> What's you're github user id? the link https://github.com/settings/keys is only useful to you. My public key is at https://github.com/mtmorgan.keys
>>>>
>>>>>
>>>>> If you believe this key was added in error, you can remove the key and disable access at the following location:
>>>>> https://github.com/settings/keys
>>>>>
>>>>>
>>>>> Now my questions are:
>>>>>
>>>>> Do you think the SSH key should look as the one I got?
>>>>>
>>>>> What did I do wrong?
>>>>>
>>>>> Why do I get: permission denied?
>>>>>
>>>>>
>>>>> Thank you.
>>>>> Best regards,
>>>>> Christian
>>>>> _._._._._._._._._._._._._._._._._._
>>>>> C.h.r.i.s.t.i.a.n S.t.r.a.t.o.w.a
>>>>> V.i.e.n.n.a A.u.s.t.r.i.a
>>>>> e.m.a.i.l: cstrato at aon.at
>>>>> _._._._._._._._._._._._._._._._._._
>>>>>
>>>>> _______________________________________________
>>>>> Bioc-devel at r-project.org mailing list
>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>
>>>>
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>
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