[Bioc-devel] Access to git repository

[Clare Pacini]

Hi all,

I am trying to commit changes to the package DrugVsDisease. I have requested 
access through the google doc. On following the instructions here:
https://bioconductor.org/developers/how-to/git/sync-existing-repositories/ 


I get the following error whilst running “git fetch —all”

Fetching origin
Fetching upstream
Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
error: Could not fetch upstream

Thanks,

Clare
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Re: [Bioc-devel] Access to git repository

[Clare Pacini]

Hi Lori,

I think I submitted a GitHub id (6 numbers) as I connected the SSH public key 
to my GitHub account. However, I will try resubmitting with the ssh-rsa key

Thanks,

Clare
> On 31 Oct 2017, at 11:21, Shepherd, Lori <lori.sheph...@roswellpark.org> 
> wrote:
> 
> The ssh key you submitted was not properly formatted.  It should start with 
> ssh-rsa.  A truncated example is 
>  ssh-rsa B3NzaC1yc2
> 
> The submitted key on the form was 6 numbers. 
> 
> Please resubmit with a properly formatted ssh-rsa key. 
> 
> 
> Lori Shepherd
> Bioconductor Core Team
> Roswell Park Cancer Institute
> Department of Biostatistics & Bioinformatics
> Elm & Carlton Streets
> Buffalo, New York 14263
> From: Bioc-devel <bioc-devel-boun...@r-project.org 
> <mailto:bioc-devel-boun...@r-project.org>> on behalf of Clare Pacini 
> <clarepac...@gmail.com <mailto:clarepac...@gmail.com>>
> Sent: Tuesday, October 31, 2017 4:37:27 AM
> To: bioc-devel@r-project.org <mailto:bioc-devel@r-project.org>
> Subject: [Bioc-devel] Access to git repository
>  
> Hi all,
> 
> I am trying to commit changes to the package DrugVsDisease. I have requested 
> access through the google doc. On following the instructions here:
> https://bioconductor.org/developers/how-to/git/sync-existing-repositories/ 
> <https://bioconductor.org/developers/how-to/git/sync-existing-repositories/> 
> <https://bioconductor.org/developers/how-to/git/sync-existing-repositories/ 
> <https://bioconductor.org/developers/how-to/git/sync-existing-repositories/>>
> 
> I get the following error whilst running “git fetch —all”
> 
> Fetching origin
> Fetching upstream
> Permission denied (publickey).
> fatal: Could not read from remote repository.
> 
> Please make sure you have the correct access rights
> and the repository exists.
> error: Could not fetch upstream
> 
> Thanks,
> 
> Clare
> [[alternative HTML version deleted]]
> 
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[Bioc-devel] Push to git not updating correctly

[Clare Pacini]

Hi all,

I have pushed changes to the DrugVsDisease repository and have been able to 
verify these changes are present in the git repository (after adding it to my 
GitHub account and checking for the changes). However, it seems that an old 
version is still be checked in the daily reports - and are reporting TIMEOUT 
issues.

Any ideas as to what I am missing here?

Thanks

Clare
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[Bioc-devel] Unable to access repository

[Clare Pacini]

Hi all,

I am the maintainer for DrugVsDisease package and am trying to push new 
changes. However, I am getting the following error:

Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.

I have previously provided an ssh key for my GitHub account with username 
clarepacini and have been able to push changes previously. I am unsure as to 
what has changed/what else I need to do?

Thanks

Clare
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Re: [Bioc-devel] Unable to access repository

[Clare Pacini]

Hi Nitesh,

There was a query about ssh keys for this package and another that I am 
maintainer on. See email chain below. I think I have been accidentally removed 
from DrugVsDisease would you be able to fix this given the information in the 
attached ?

Thanks

Clare

—


From: "Obenchain, Valerie" <valerie.obench...@roswellpark.org>
Subject: Re: Bioconductor package access
Date: 6 February 2018 at 22:23:39 GMT
To: Clare Pacini <clarepac...@gmail.com>
Cc: "saezrodrig...@ebi.ac.uk" <saezrodrig...@ebi.ac.uk>

On 02/06/2018 02:19 PM, Obenchain, Valerie wrote:
> Thanks Clare.
> 
> I have change the ssh key over to c.pacini and will add your github username 
> to the new account. You should now have access to both packages with that key.
> 
> Now that the key is moved over, j.saezrodriguz will have no access. Julio, 
> please go to the link below and add your github username or ssh key. Be sure 
> to use the email saezrodrig...@ebi.ac.uk <mailto:saezrodrig...@ebi.ac.uk> and 
> username j.saezrodriguz.

Oops, forgot the 'e'.  I meant 'j.saezrodriguez'.

Valerie
> 
> https://docs.google.com/forms/d/e/1FAIpQLSdlTbNjsQJDp0BA480vo4tNufs0ziNyNmexegNZgNieIovbAA/viewform
>  
> <https://docs.google.com/forms/d/e/1FAIpQLSdlTbNjsQJDp0BA480vo4tNufs0ziNyNmexegNZgNieIovbAA/viewform>
> 
> Valerie
> 
> 
> 
> 
> 
> 
> On 02/06/2018 01:48 PM, Clare Pacini wrote:
>> Hi Valerie,
>> 
>> Thanks for your email. Yes I would like to keep access to both packages, 
>> Julio will require access just to DrugVsDisease.
>> The ssh key is mine and my GitHub username is clarepacini.
>> 
>> Thanks,
>> 
>> Clare
>>> On 6 Feb 2018, at 21:18, Obenchain, Valerie 
>>> <valerie.obench...@roswellpark.org 
>>> <mailto:valerie.obench...@roswellpark.org>> wrote:
>>> 
>>> Hi Clare,
>>> 
>>> There is some confusion between credentials for users c.pacini and 
>>> j.saezrodriguz. A number of combinations of usernames, emails and ssh keys 
>>> for these 2 users were entered in the Google Sheet. We also have historical 
>>> data for these users from svn. I'd like to clean this up if possible.
>>> 
>>> 1) accounts 
>>> 
>>> Do you want accounts for both c.pacini and j.saezrodriguez? For each 
>>> account, we need several pieces of information. Here is what we currently 
>>> have:
>>> 
>>> username : c.pacini
>>> email: clarepac...@gmail.com <mailto:clarepac...@gmail.com>
>>> github username: none
>>> ssh keys: none
>>> 
>>> username: j.saezrodriguez
>>> email: saezrodrig...@ebi.ac.uk <mailto:saezrodrig...@ebi.ac.uk>
>>> github username: none
>>> ssh keys: ssh-rsa B3NzaC1yc2EA ... 5pTvNvU2MiGd1BaJw== 
>>> clarepac...@gmail.com <mailto:clarepac...@gmail.com>
>>> 
>>> 2) package access
>>> 
>>> Currently user c.pacini has access to covEB and user j.saezrodriguez has 
>>> access to DrugVsDisease. Is this correct? Because we only have keys for 
>>> j.saezrodriguez and none for c.pacini, no one can access covEB.
>>> 
>>> If you are both active maintainers you should have separate accounts and 
>>> both be listed on both packages. If you have a github usernames please 
>>> provide those so we can get ssh keys from there.
>>> 
>>> Let me know if you have questions.
>>> 
>>> Valerie
>>> 
>>> This email message may contain legally privileged and/or confidential 
>>> information. If you are not the intended recipient(s), or the employee or 
>>> agent responsible for the delivery of this message to the intended 
>>> recipient(s), you are hereby notified that any disclosure, copying, 
>>> distribution, or use of this email message is prohibited. If you have 
>>> received this message in error, please notify the sender immediately by 
>>> e-mail and delete this email message from your computer. Thank you.
>> 
> 


This email message may contain legally privileged and/or confidential 
information. If you are not the intended recipient(s), or the employee or agent 
responsible for the delivery of this message to the intended recipient(s), you 
are hereby notified that any disclosure, copying, distribution, or use of this 
email message is prohibited. If you have received this message in error, please 
notify the sender immediately by e-mail and delete this email message from your 
computer. Thank you. 


> On 11 Apr 2018, at 17:40, Turaga, Nitesh <nitesh.tur...@roswellpark.org> 
> wrote:
> 
> Hi, 
&

[Bioc-devel] Commits not appearing in bioconductor build

[Clare Pacini]

Hi all,

I have pushed some changes to a package DrugVsDisease but after 2 builds on 
bioconductor it is not showing any updates to the package. Any suggestions? 

Thanks

Clare

dhcp-10-248-132-213:DrugVsDisease clare$ git commit -m "add import From"
[master c8faca2] add import From
 1 file changed, 2 insertions(+)
dhcp-10-248-132-213:DrugVsDisease clare$ git add DESCRIPTION 
dhcp-10-248-132-213:DrugVsDisease clare$ git commit -m "bump version"
[master a2d6b1b] bump version
 1 file changed, 2 insertions(+), 2 deletions(-)
dhcp-10-248-132-213:DrugVsDisease clare$ git push upstream master
Counting objects: 12, done.
Delta compression using up to 8 threads.
Compressing objects: 100% (12/12), done.
Writing objects: 100% (12/12), 1.45 KiB | 1.45 MiB/s, done.
Total 12 (delta 6), reused 0 (delta 0)
To git.bioconductor.org:packages/DrugVsDisease.git
   86ac1a1..a2d6b1b  master -> master
dhcp-10-248-132-213:DrugVsDisease clare$ git push origin master
Counting objects: 6, done.
Delta compression using up to 8 threads.
Compressing objects: 100% (6/6), done.
Writing objects: 100% (6/6), 737 bytes | 737.00 KiB/s, done.
Total 6 (delta 3), reused 0 (delta 0)
remote: Resolving deltas: 100% (3/3), completed with 2 local objects.
To https://github.com/clarepacini/DrugVsDisease.git
   8ce514c..a2d6b1b  master -> master
dhcp-10-248-132-213:DrugVsDisease clare$ git push upstream master
Everything up-to-date


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