[Bioc-devel] EXTERNAL: Re: Cannot move 'xps' to GIT
cstrato
cstrato at aon.at
Fri Oct 13 20:07:02 CEST 2017
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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