[Bioc-devel] EXTERNAL: Re: Cannot move 'xps' to GIT
cstrato
cstrato at aon.at
Mon Oct 16 00:00:20 CEST 2017
I have just seen the update 2017-10-15 of the BUILD/CHECK report:
http://bioconductor.org/checkResults/devel/bioc-LATEST/xps/
which was not available when I have sent my former mail.
For some reason my commit to version xps_1.37.2 was not accepted.
Please tell me what I need to do to solve this problem.
Best regards,
Christian
On 10/15/17 21:37, cstrato wrote:
> Hi,
>
> Since 'https://github.com/cstrato/xps' does only contain information how
> to create or push a repository I tried to follow again:
>
>
> http://master.bioconductor.org/developers/how-to/git/push-to-github-bioc/
>
>
> 2. View existing remotes
> $ 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)
>
>
> 3. Make and commit changes to the master branch
> $ git checkout master
> M DESCRIPTION
> M NEWS
> M configure.in
> Already on 'master'
> Your branch is up-to-date with 'origin/master'.
> # edit files, etc.
> $ git add -v DESCRIPTION
> $ git add -v NEWS
> $ git add -v configure.in
>
>
>
> When running 'commit' I got the following information, which is not
> clear to me:
>
> $ git commit -m "update for configure.in"
> [master 7a9855f] update for configure.in
> Committer: rabbitus <rabbitus at lumimacs-iMac.local>
> Your name and email address were configured automatically based
> on your username and hostname. Please check that they are accurate.
> You can suppress this message by setting them explicitly. Run the
> following command and follow the instructions in your editor to edit
> your configuration file:
>
> git config --global --edit
>
> After doing this, you may fix the identity used for this commit with:
>
> git commit --amend --reset-author
>
> 3 files changed, 62 insertions(+), 58 deletions(-)
>
>
>
> So I tried:
>
> $ git config --global --edit
> # This is Git's per-user configuration file.
> [user]
> # Please adapt and uncomment the following lines:
> # name = rabbitus
> # email = rabbitus at lumimacs-iMac.local
>
>
> and changed the '.gitconfig' file to:
> # This is Git's per-user configuration file.
> [user]
> # Please adapt and uncomment the following lines:
> # name = cstrato
> # email = cstrato at aon.at
>
>
>
> It is not clear to me whether I have to change my name/email or keep the
> original one.
>
> Could you tell me which one should be the correct one?
>
>
>
> Then I did run:
>
> $ git commit --amend --reset-author
> # Please enter the commit message for your changes. Lines starting
> # with '#' will be ignored, and an empty message aborts the commit.
> #
> # Committer: rabbitus <rabbitus at lumimacs-iMac.local>
> #
> # On branch master
> # Your branch is ahead of 'origin/master' by 1 commit.
> # (use "git push" to publish your local commits)
> #
> # Changes to be committed:
> # modified: DESCRIPTION
> # modified: NEWS
> # modified: configure.in
>
>
> In this case I did not change anything, since I am not sure what it means.
>
> Can you explain what this means, since
> 'https://git-scm.com/docs/git-commit' did not help me.
>
> Should I change this file?
>
>
>
> Then I did steps 5 and 6 and got the following:
>
> 5. Push updates to GitHub's (origin) master branch
> $ 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.
>
>
> 6. Next, push updates to Bioconductor's (upstream) master branch
> $ git push upstream master
> Enter passphrase for key '/Users/rabbitus/.ssh/id_rsa':
> Counting objects: 5, done.
> Delta compression using up to 8 threads.
> Compressing objects: 100% (5/5), done.
> Writing objects: 100% (5/5), 727 bytes | 0 bytes/s, done.
> Total 5 (delta 4), reused 0 (delta 0)
> To git.bioconductor.org:packages/xps.git
> d63ffaf..d83779f master -> master
>
>
>
> Finally I did:
>
> $ ssh -v git at git.bioconductor.org/packages/xps
> OpenSSH_7.4p1, LibreSSL 2.5.0
> debug1: Reading configuration data /Users/rabbitus/.ssh/config
> debug1: Reading configuration data /etc/ssh/ssh_config
> ssh: Could not resolve hostname git: nodename nor servname provided, or
> not known
>
>
> However, now I get only an ssh error message:
>
>
> Do you know what I did wrong this time?
>
>
> Thank you.
> Best 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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