________________________________
From: Vladislav Petyuk <pet...@gmail.com>
Sent: Tuesday, October 10, 2017 2:56 PM
To: Van Twisk, Daniel
Subject: EXTERNAL: Re: MSnID failing on release and devel
I submitted my SSH RSA key back on Friday evening.
made sure that I have upstream in .git/config
[remote "upstream"]
url = g...@git.bioconductor.org:packages/MSnID.git
fetch = +refs/heads/*:refs/remotes/upstream/*
But still can't fetch "upstream". What am I missing (if anything)?
WE33801:MSnID d3m629$ 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
WE33801:MSnID d3m629$
On Fri, Oct 6, 2017 at 7:15 AM Van Twisk, Daniel
<daniel.vantw...@roswellpark.org<mailto:daniel.vantw...@roswellpark.org>> wrote:
MSnID is a package that has been on Biocondcutor for three years, so there is
no reason to set up a webhook as described in the "adding-a-web-hook" section
in contributions. The Bioconductor Mirror that you referred to
(https://github.com/Bioconductor-mirror/MSnID) is deprecated and will no longer
reflect further changes to your package. I can see that you've recently made
new commits to your package on your github repository. To push the changes on
the Bioconductor git server, you must first complete this Google form, if you
have not already done so, so that you can have write access to your package on
the BIoconductor git server
(https://docs.google.com/forms/d/e/1FAIpQLSdYJ86-qpStdbbcPzFFXO4_XWnN8DvF2dOgNLE_iWNd0J-g8g/viewform).
Once this is done, you need to follow the instructions at this link to sync
your existing git repository to the server's
https://master.bioconductor.org/developers/how-to/git/sync-existing-repositories/.
[https://lh4.googleusercontent.com/aw68Dl1RAj_x7Ub4askJuRpQYDopphhllaweY9qUhJUjm2rblsz_BOrqXW1Zk_lQUcA=w1200-h630-p]<https://docs.google.com/forms/d/e/1FAIpQLSdYJ86-qpStdbbcPzFFXO4_XWnN8DvF2dOgNLE_iWNd0J-g8g/viewform>
Bioconductor SSH
keys<https://docs.google.com/forms/d/e/1FAIpQLSdYJ86-qpStdbbcPzFFXO4_XWnN8DvF2dOgNLE_iWNd0J-g8g/viewform>
docs.google.com<http://docs.google.com>
This form allows Bioconductor developers to submit SSH keys for access to their
Bioconductor git repository.
________________________________
From: Vladislav Petyuk <pet...@gmail.com<mailto:pet...@gmail.com>>
Sent: Friday, October 6, 2017 2:56:05 AM
To: Van Twisk, Daniel
Subject: Re: MSnID failing on release and devel
Daniel, could you help to sort out the following problem?
I created webhook as described here
https://github.com/Bioconductor/Contributions#adding-a-web-hook
However, the test delivery didn't do through.
https://github.com/vladpetyuk/MSnID/settings/hooks/16670279#delivery-response
It says "400 Bad Request"
I'd appreciated any pointers,
Vlad
On Thu, Oct 5, 2017 at 12:59 PM Vladislav Petyuk
<pet...@gmail.com<mailto:pet...@gmail.com>> wrote:
I believe before it was set though webhook. Now it is a bit different. I'll
try to sort it out
http://master.bioconductor.org/developers/how-to/git/maintain-github-bioc/
On Thu, Oct 5, 2017 at 12:45 PM Vladislav Petyuk
<pet...@gmail.com<mailto:pet...@gmail.com>> wrote:
The problem is fixed.
I apologize if I lost track how Bioconductor packages are updated. It used to
be that once the commit pushed to GitHub it is propagated to Bioconductor's
GitHub.
The code is updated on my account, but not on Bioconductors (after 30 min wait
time).
https://github.com/vladpetyuk/MSnID
https://github.com/Bioconductor-mirror/MSnID
Please suggest how to make sure the code fix gets into Bioconductor repo.
Thanks,
Vlad
On Fri, Sep 29, 2017 at 1:05 PM Vladislav Petyuk
<pet...@gmail.com<mailto:pet...@gmail.com>> wrote:
Will try. Thanks for bringing this to my attention, Vlad
On Fri, Sep 29, 2017 at 1:01 PM Van Twisk, Daniel
<daniel.vantw...@roswellpark.org<mailto:daniel.vantw...@roswellpark.org>> wrote:
Hello,
I am a member of the Bioconductor core team and am emailing you to notify you
that a package you are maintaining, MSnID, is failing on our release and devel
single package builders:
https://www.bioconductor.org/checkResults/release/bioc-LATEST/MSnID/veracruz2-buildsrc.html
&
https://www.bioconductor.org/checkResults/devel/bioc-LATEST/MSnID/veracruz1-buildsrc.html.
Version 3.6 of Bioconductor is coming soon and we would like the release to
be free of errors. In addition, If your package is failing on the release
branch, these failures will be cemented into version 3.5 of Bioconductor. For
these reasons, we ask you make the fixes to your package by mid-October. If
you have any question, please don't hesitate to reply.
Thank you.
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