[Bioc-devel] EXTERNAL: Re: Cannot move 'xps' to GIT
cstrato
cstrato at aon.at
Sat Oct 14 13:29:38 CEST 2017
Dear Turaga,
As you suggested, I did:
$ git remote set-url origin git at github.com:cstrato/xps.git
$ git remote -v
origin git at github.com:cstrato/xps.git (fetch)
origin git at github.com:cstrato/xps.git (push)
upstream git at git.bioconductor.org:packages/xps.git (fetch)
upstream git at git.bioconductor.org:packages/xps.git (push)
However, now I can no longer do:
$ git push origin master
Permission denied (publickey).
fatal: Could not read from remote repository.
Please make sure you have the correct access rights
and the repository exists.
My repository https://github.com/cstrato/xps is still empty.
Do you know what the problem might be?
Could it be that the 'git/svn transition: ssh keys' form did not accept
my SSH public key?
Or could it be that I am running Firefox in 'private browsing' mode
(although cookies are activated)?
To test this I have just turned off the 'private browsing' mode and
resubmitted my SSH public key to 'git/svn transition: ssh keys'. The
form now displays:
Thanks for providing your ssh key; access should be enabled in 1
business day.
Now the reply email from the Google form does indeed display my correct
ssh key.
Maybe, you should mention in the 'howto' that the private browsing mode
need to be turned off, too, in addition to the need to allow cookies.
(Firefox 56.0 does allow to activate cookies even when in private
browsing mode!)
BTW, I tried to follow 'bioconductor.org/developers/how-to/git/'. It
contains 12 links to other sites, and sometimes it is not clear to me
how to proceed further.
Now I have checked it once again, but for some reason I did not find the
command 'git remote set-url origin ...' that you suggested on any of the
12 links.
Maybe I missed it?
Regards,
Christian
On 10/13/17 20:12, Turaga, Nitesh wrote:
> 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
>>>>>> _._._._._._._._._._._._._._._._._._
>>>>>>
>>>>>> _______________________________________________
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>>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>>
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