Re: [Bioc-devel] failing Biocondcutor package STAN

[Turaga, Nitesh]

Hi,

Your key on file is 

ssh-rsa 
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

Are you using a private key which corresponds to this public key? If you have 
changed your PC, you should move the previous key to your new PC. 

If that is not available, you should submit to the google form. Please check 
http://bioconductor.org/developers/how-to/git/ (FAQ #3) for more information on 
how to submit you keys.

Best,

Nitesh


> On Mar 16, 2018, at 1:51 PM, campos  wrote:
> 
> Dear Bioconductor team,
> 
> I am having some problems with pushing the changes of the package STAN 
> to the master brunch.
> 
> I recently have changed my PC and I am trying to connect to the 
> bioconductor package but I get the following error:
> 
> Permission denied (publickey).
> fatal: Could not read from remote repository.
> 
> my remote origin is: g...@git.bioconductor.org:packages/STAN 
> 
> 
> my username is r.campos
> 
> and my github account is rfael0cm
> 
> 
> Could you help me?
> 
> I am really sorry but I am not experienced in github.
> 
> Regards,
> 
> Rafael
> 
> 
> 
> 
> 
> 
>  Forwarded Message 
> Subject:  Re: failing Biocondcutor package STAN
> Date: Fri, 16 Mar 2018 17:47:53 +
> From: Shepherd, Lori 
> To:   campos 
> 
> 
> 
> No problem at all but please post to
> 
> 
> bioc-devel@r-project.org
> 
> 
> Include the commands you are trying with relevant output
> 
> 
> 
> Lori Shepherd
> 
> Bioconductor Core Team
> 
> Roswell Park Cancer Institute
> 
> Department of Biostatistics & Bioinformatics
> 
> Elm & Carlton Streets
> 
> Buffalo, New York 14263
> 
> 
> *From:* campos 
> *Sent:* Friday, March 16, 2018 1:45:04 PM
> *To:* Shepherd, Lori
> *Subject:* Re: failing Biocondcutor package STAN
> 
> Hi Lori,
> 
> 
> I am really sorry but I got completely lost again. I connected my 
> account but somehow pushed don't work... it says that my remote origin 
> is: g...@git.bioconductor.org:packages/STAN 
> 
> 
> Could you help me?
> 
> Thank you very much,
> 
> Rafael
> 
> 
> On 16.03.2018 14:52, Shepherd, Lori wrote:
>> 
>> You'll have to submit the new key to the form
>> 
>> 
>> https://docs.google.com/forms/d/1CCwUhjtG82rnmcTWYqY43WcmBx5YyQm5UD4pcs1dhEs/viewform?edit_requested=true
>> 
>> with the username r.campos
>> 
>> 
>> There is a link for key generation at the top of the form.
>> 
>> 
>> For further key assistance please ask on the bioc-devel@r-project.org 
>>  mailing list as there are other 
>> members on the team that are better apt to handle key questmy remote 
>> origin is: g...@git.bioconductor.org:packages/STAN 
>> ions.
>> 
>> 
>> 
>> Lori Shepherd
>> 
>> Bioconductor Core Team
>> 
>> Roswell Park Cancer Institute
>> 
>> Department of Biostatistics & Bioinformatics
>> 
>> Elm & Carlton Streets
>> 
>> Buffalo, New York 14263
>> 
>> 
>> *From:* campos  
>> *Sent:* Friday, March 16, 2018 9:40:49 AM
>> *To:* Shepherd, Lori
>> *Subject:* Re: failing Biocondcutor package STAN
>> 
>> Hi Lori,
>> 
>> 
>> I just realized that I am on a new PC now and my public Key does not 
>> work anymore. Could you please guide me through creating a new one so 
>> I can push the changes/
>> 
>> Thank you very much,
>> 
>> Rafael
>> 
>> 
>> On 16.03.2018 14:39, Shepherd, Lori wrote:
>>> 
>>> Yes the normal process:
>>> 
>>> 
>>> You would `git rm` any offending files
>>> 
>>> Do a version bump in the Description file
>>> 
>>> Commit the changes `git commit -a`
>>> 
>>> Then `git�push upstream master`
>>> 
>>> 
>>> Lori Shepherd
>>> 
>>> Bioconductor Core Team
>>> 
>>> Roswell Park Cancer Institute
>>> 
>>> Department of Biostatistics & Bioinformatics
>>> 
>>> Elm & Carlton Streets
>>> 
>>> Buffalo, New York 14263
>>> 
>>> 
>>> *From:* campos  
>>> *Sent:* 

[Bioc-devel] amplican tokay2 i386 error

[Kornel Labun]

Hi,

Could you help me diagnose what is wrong with my package, amplican, that
fails to pass check on tokay2 i386?

I fail to understand what might be wrong from the report
http://bioconductor.org/checkResults/devel/bioc-LATEST/amplican/tokay2-checksrc.html
.
It is long standing problem, since the first moment we moved into devel
3.7. I think it might be related to my data.table package which I import as
I have tried to comment out some tests and examples, but it seems I am
running in circle.

Best,
Kornel Labun

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Re: [Bioc-devel] updating experiment data package MethylAidData

[Shepherd, Lori]

Yes it can be treated the same as a software package. You would have to push to 
git.bioconductor.org with a version bump for it to propagate to our system.  
Your ssh key will have to be submitted and the appropriate maintainer user id 
will have to be associated with the package just as the software package to 
have access to push.



https://docs.google.com/forms/d/1CCwUhjtG82rnmcTWYqY43WcmBx5YyQm5UD4pcs1dhEs/viewform?edit_requested=true




Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Davy Cats 

Sent: Thursday, March 15, 2018 9:44:36 AM
To: bioc-devel@r-project.org
Cc: mviter...@gmail.com
Subject: [Bioc-devel] updating experiment data package MethylAidData

Dear all,

We are looking to update the MethylAidData experiment data package by
adding an additional dataset. We are not sure what the appropriate steps
towards this are. Can we just update the package and push to the
bioconductor git with a version bump (like with a software package)? Or is
there some other process here?

Best regards,
Davy

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[Bioc-devel] Question about Wercker continuous integration

[Kevin RUE]

Dear all,

I'm usually a big Travis CI fan, but I'm having a go at Wercker, using the
bioconductor/devel_core2 docker (I have also tried the rocker 'parent' ones
without further success).
I am running into the following issue:

[...]
* creating vignettes ... ERROR
Error: processing vignette 'NewPackage-vignette.Rmd' failed with
diagnostics:
package ‘backports’ was installed by an R version with different internals;
it needs to be reinstalled for use with this R version
Execution halted
Error: Command failed (1)
In addition: Warning message:
`cleanup` is deprecated
Execution halted
Check Failed, dumping logs
find: ‘./*.Rcheck’: No such file or directory
failed: Check Failed

I've tried adding a task that re-installs the `backports` package from
source (CRAN), but I still get the same error.

My wercker.yml looks like:
box: bioconductor/devel_core2
build:
steps:
- script:
name: Install devtools
code: R -e "install.packages('devtools')"
- script:
name: Install backports
code: R -e "install.packages('backports')"
- jimhester/r-dependencies
- jimhester/r-check
- jimhester/r-lint
- jimhester/r-coverage



Any help/advice/experience with Wercker would be greatly appreciated!

Best wishes,
Kevin

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Re: [Bioc-devel] Applying changes to existing package

[Shepherd, Lori]

you can also check the build and check status on out systems off the daily 
build reports.  It normally can take up to 24 hours for changes to appear but 
you should see the version number bump.


http://bioconductor.org/checkResults/


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Sean Davis 

Sent: Friday, March 16, 2018 6:31:04 AM
To: Christian Oertlin
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Applying changes to existing package

Hi, Christian.

There is not yet a browsable version of the Bioconductor git repository.
The way to check git.bioconductor.org status is, as you noted, to work with
a checkout of the repository locally. If you'd like a more visual view of
your local checkout, you might take a look at one of several desktop
repository browsers.

Sean

On Fri, Mar 16, 2018 at 5:53 AM Christian Oertlin 
wrote:

> Hello everyone,
>
> I am the maintainer of the anota2seq package.  The package was accepted
> for release 3.6 and is on the bioconductor webpage.
>
> I had minor updates for the package which I pushed to the github
> repositories by following the steps here:
> https://bioconductor.org/developers/how-to/git/sync-existing-repositories/
>
> I can see the changes in my github webpage ChrOertlin/anota2seq/
>
> This might be a very naive question. When I follow to
> https://git.bioconductor.org/ I can find the package as listed. Is there
> a way to see the contents of that repository other from changing into the
> upstream git branch locally, for example a website like my personal github
> account? Just to check if everything is in the right place in a more visual
> way...
>
>
> Cheers,
> Christian
>
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>
> ___
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>
--
--
Sean Davis, MD, PhD
Center for Cancer Research
National Cancer Institute
National Institutes of Health
Bethesda, MD 20892
https://seandavi.github.io/
https://twitter.com/seandavis12

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