[Bioc-devel] Fw: EXTERNAL: Re: MSnID failing on release and devel

Tue Oct 10 21:57:01 CEST 2017

________________________________
From: Vladislav Petyuk <petyuk at 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 = git at 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.VanTwisk at roswellpark.org<mailto:Daniel.VanTwisk at 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 <petyuk at gmail.com<mailto:petyuk at 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 <petyuk at gmail.com<mailto:petyuk at 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 <petyuk at gmail.com<mailto:petyuk at 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 <petyuk at gmail.com<mailto:petyuk at 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.VanTwisk at roswellpark.org<mailto:Daniel.VanTwisk at 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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