Re: [Bioc-devel] Duplicate Commits in ASSIGN Package

[Turaga, Nitesh]

Hi David,

I can take a look at your package later today on your Github and update the 
version on Bioconductor if everything looks good. 

The reason you are not able to push is because we prevent “force” pushes on the 
bioconductor git server from maintainers.

Give me sometime and I’ll get back to you.

Best,

Nitesh 


> On Jan 24, 2018, at 12:48 PM, Jenkins, David  wrote:
> 
> Hi All,
> 
> I’m the maintainer of the ASSIGN package. It’s currently failing the devel 
> build and when I tried to push a fix for that I noticed that we have a lot of 
> duplicate commits in the history from a while back, I think from the git-svn 
> bridge.
> 
> I rebased and removed all of the duplicate commits and the deduped version is 
> on our github:
> 
> https://github.com/compbiomed/ASSIGN
> 
> Can you help me replace the duplicated version with the new version?
> 
> Thanks,
> 
> David
> 
>   [[alternative HTML version deleted]]
> 
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[Bioc-devel] NanoStringDiff package update

[Zhai, Tingting]

I’m one of the maintainers of NanoStringDiff package on Bioconductor. Now I
want to update this package and add some useful functions. I’m using SVN,
but when committing, it gives me this error: The new canonical location for
Bioconductor software and

data experiment packages is git.bioconductor.org


The recommended way to maintain your Bioconductor software

or data experiment package is to use GitHub.



Does this mean I’m not able to use SVN to maintain my package any more? I’m
not familiar with github.


Thank you very much for any help in advance.


Best wishes,

Tingting

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[Bioc-devel] not all bioc packages visible on github?

[Paul Shannon]

By example:

https://github.com/Bioconductor/KEGGREST-> github project homepage displays
https://github.com/Bioconductor/BrowserViz  -> 404

Yet this works fine:

  git clone g...@git.bioconductor.org:packages/BrowserViz.git

Is visibility at github.com/Bioconductor therefore conditional?   

My overall goal is to fork the BrowserViz repo, create a v2.0.0 branch, merge 
back into devel after extensive refactoring.

Advice welcome!

Thank you.

 - Paul

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Re: [Bioc-devel] not all bioc packages visible on github?

[Robert M. Flight]

Paul,

My understanding was that the Bioconductor github repos were going to die,
and it was up to the maintainer where the source was, and a public source
need not be available. I asked about this previously, and there was too
much confusion between the official Bioconductor repos and developers
personal repos, I believe (Nitesh or others please correct me if I've
gotten the details wrong).

Hope that helps,

-Robert

On Wed, Jan 24, 2018 at 8:27 PM Paul Shannon <
paul.thurmond.shan...@gmail.com> wrote:

> By example:
>
> https://github.com/Bioconductor/KEGGREST-> github project homepage
> displays
> https://github.com/Bioconductor/BrowserViz  -> 404
>
> Yet this works fine:
>
>   git clone g...@git.bioconductor.org:packages/BrowserViz.git
>
> Is visibility at github.com/Bioconductor therefore conditional?
>
> My overall goal is to fork the BrowserViz repo, create a v2.0.0 branch,
> merge back into devel after extensive refactoring.
>
> Advice welcome!
>
> Thank you.
>
>  - Paul
>
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Re: [Bioc-devel] Permission denied when fetching from BioC GitHub repository

[Federico C]

Hi Nitesh,

thanks a lot for your message. It makes perfect sense.

Best wishes,

Federico

> On 24 Jan 2018, at 17:33, Turaga, Nitesh  
> wrote:
> 
> Hi 
> 
> Only packages maintained by Bioconductor are at that location 
> gitHub.com/Bioconductor.  Your package is not maintained by the core-team in 
> Bioconductor, so, it does not belong in that location.
> 
> We follow the same process as all the maintainers, we have a Github repo to 
> take advantage of the social coding practices, and the canonical Bioconductor 
> git server which acts as the central server for bioconductor packages.
> 
> I hope this answers your question.
> 
> Best,
> 
> Nitesh 
> 
>> On Jan 24, 2018, at 11:24 AM, Federico C  wrote:
>> 
>> Hi Valerie,
>> 
>> the ssh key has now been setup and it works. I had some issues with merging 
>> but at the end I decided to force BioC master to GitHub master (following 
>> https://bioconductor.org/developers/how-to/git/abandon-changes/#force-bioconductor--to-github-
>>  
>> ).
>>  Afterwards, I pushed the bug fix to both origin and upstream remotes 
>> (master branch). Indeed:
>> 
>> | => git status
>> On branch master
>> Your branch is up-to-date with 'upstream/master'.
>> 
>> nothing to commit, working tree clean
>> 
>> However, shouldn’t wavClusteR be listed at https://github.com/Bioconductor 
>>  at this point?
>> 
>> Thanks a lot for your help.
>> Best wishes,
>> 
>> Federico
>> 
>> 
>> 
>> 
>> 
>>> On 23 Jan 2018, at 20:50, Federico C  wrote:
>>> 
>>> Hi Valerie,
>>> 
>>> done. Thanks a lot,
>>> 
>>> Federico
>>> 
 On 23 Jan 2018, at 20:18, Obenchain, Valerie 
 > wrote:
 
 Hi Federico,
 
 We don't have an ssh key on file for you. Please add one by following 
 instructions at the link below and use the ID of 'f.comoglio':
 
 https://docs.google.com/forms/d/e/1FAIpQLSdlTbNjsQJDp0BA480vo4tNufs0ziNyNmexegNZgNieIovbAA/viewform
  
 
 
 You will get an email in the next 24 hours if the submission was 
 successful.
 
 Valerie
 
 On 01/23/2018 09:47 AM, Federico C wrote:
> Dear all,
> 
> I’m trying to push a bug fix for wavClusteR to the BioC GitHub 
> repository. I currently pushed the latest package version to the devel 
> and master branch of my GitHub repository 
> (https://github.com/FedericoComoglio/wavClusteR 
>  
>  
> ).
> 
> To sync these changes with the bioC GitHub repository, I have followed 
> the documentation at https://bioconductor.org/developers/how-to/git/ 
>  
>  
>  . However, even though 
> I added an upstream remote to my repository and added a public key as 
> described, when I fetch updates from all (see 
> https://bioconductor.org/developers/how-to/git/sync-existing-repositories/
>  
> 
>  
> 
>  
> )
>  I get
> 
> | => git fetch --all
> Fetching origin
> Fetching upstream
> g...@git.bioconductor.org  
>  : 
> 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
> 
> Could you please help me with this issue?
> 
> Thanks a lot for your time and patience.
> 
> Best wishes,
> Federico
>   [[alternative HTML version deleted]]
> 
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[Bioc-devel] Duplicate Commits in ASSIGN Package

[Jenkins, David]

Hi All,

I’m the maintainer of the ASSIGN package. It’s currently failing the devel 
build and when I tried to push a fix for that I noticed that we have a lot of 
duplicate commits in the history from a while back, I think from the git-svn 
bridge.

I rebased and removed all of the duplicate commits and the deduped version is 
on our github:

https://github.com/compbiomed/ASSIGN

Can you help me replace the duplicated version with the new version?

Thanks,

David

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Re: [Bioc-devel] Permission denied when fetching from BioC GitHub repository

[Federico C]

Hi Valerie,

the ssh key has now been setup and it works. I had some issues with merging but 
at the end I decided to force BioC master to GitHub master (following 
https://bioconductor.org/developers/how-to/git/abandon-changes/#force-bioconductor--to-github-
 
).
 Afterwards, I pushed the bug fix to both origin and upstream remotes (master 
branch). Indeed:

| => git status
On branch master
Your branch is up-to-date with 'upstream/master'.

nothing to commit, working tree clean

However, shouldn’t wavClusteR be listed at https://github.com/Bioconductor 
 at this point?

Thanks a lot for your help.
Best wishes,

Federico





> On 23 Jan 2018, at 20:50, Federico C  wrote:
> 
> Hi Valerie,
> 
> done. Thanks a lot,
> 
> Federico
> 
>> On 23 Jan 2018, at 20:18, Obenchain, Valerie 
>> > > wrote:
>> 
>> Hi Federico,
>> 
>> We don't have an ssh key on file for you. Please add one by following 
>> instructions at the link below and use the ID of 'f.comoglio':
>> 
>> https://docs.google.com/forms/d/e/1FAIpQLSdlTbNjsQJDp0BA480vo4tNufs0ziNyNmexegNZgNieIovbAA/viewform
>>  
>> 
>> 
>> You will get an email in the next 24 hours if the submission was successful.
>> 
>> Valerie
>> 
>> On 01/23/2018 09:47 AM, Federico C wrote:
>>> Dear all,
>>> 
>>> I’m trying to push a bug fix for wavClusteR to the BioC GitHub repository. 
>>> I currently pushed the latest package version to the devel and master 
>>> branch of my GitHub repository 
>>> (https://github.com/FedericoComoglio/wavClusteR 
>>>  
>>>  
>>> ).
>>> 
>>> To sync these changes with the bioC GitHub repository, I have followed the 
>>> documentation at https://bioconductor.org/developers/how-to/git/ 
>>>  
>>>  
>>>  . However, even though I 
>>> added an upstream remote to my repository and added a public key as 
>>> described, when I fetch updates from all (see 
>>> https://bioconductor.org/developers/how-to/git/sync-existing-repositories/ 
>>> 
>>>  
>>> 
>>>  
>>> )
>>>  I get
>>> 
>>> | => git fetch --all
>>> Fetching origin
>>> Fetching upstream
>>> g...@git.bioconductor.org  
>>>  : 
>>> 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
>>> 
>>> Could you please help me with this issue?
>>> 
>>> Thanks a lot for your time and patience.
>>> 
>>> Best wishes,
>>> Federico
>>> [[alternative HTML version deleted]]
>>> 
>>> ___
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>>> 
>> 
>> 
>> 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.
> 


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