[Bioc-devel] Having problems pushing changes to Bioconductor...

[Kern, Lori]

Sure these sections would probably be useful in your situation.

pushing to github and bioconductor
http://contributions.bioconductor.org/git-version-control.html#push-to-github-bioc

And
fixing bugs in release and devel
http://contributions.bioconductor.org/git-version-control.html#bug-fix-in-release-and-devel


Cheers,




Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Paul Brennan <brennanpincardiff using gmail.com>
Sent: Wednesday, March 6, 2024 1:03 PM
To: Kern, Lori <Lori.Shepherd using RoswellPark.org>
Cc: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] Having problems pushing changes to Bioconductor...

Dear Lori,
    Thanks for your prompt and helpful email.
    I think I've managed to make the necessary changes to stop the build error.
    I think it did it quite manually changing my Github, the Bioconductor dev code and the Bioconductor RELEASE_3_18 for drawProteins.
    The way I did it felt a bit hacky but I'm hoping it will work.
    I did have to set up new SSH - so thanks for the pointers for that too.
    If you have a moment and you can point me towards a resource that makes it more obvious how to push code changes from Github -> dev -> release, I would be grateful. I feel sure the advice is somewhere there and I just don't understand it or utilise it properly.
    Well thanks again,
Paul

On Wed, Mar 6, 2024 at 2:23 PM Kern, Lori <Lori.Shepherd using roswellpark.org<mailto:Lori.Shepherd using roswellpark.org>> wrote:
Could you please show the commands you are trying along with a
git remote -v


I've check the configuration on our end and everything looks correct. You'll need to make sure you are pointing to one of the uploaded ssh keys on the BiocCredentials account (or create a new one if you are on a different machine)
There is useful information found at
http://contributions.bioconductor.org/git-version-control.html#new-package-workflow<http://secure-web.cisco.com/1QxkeTBgOjDQWowLH33SIzsQ5nwdfnitZGgHfL1nKsLZD7BtJWaMk-UfR1Y1h_BZGthvWZUWWw6AiX_yGntIck11RQDneK0ND5RBdZU7ZDDwDAs4EGTWoIWevk5_ShFCXbzv3K61_rVu52TDhufaPHHQnNy2obIOA-ZKzCnYs-A5baSlyCGK1Yw1L5pWuzcpq1MZY21fVWsOHpB6MgmiCOlTFjQ-16fw8JyrXVzbEpXbGA0c27yb4qnxpNet0MC1o12G013E71Q5tz5Nv1iJ9BuNZoPTtabZHKKLfhNkmHSwykhHzQNKVT2wxJyfGItHk/http%3A%2F%2Fcontributions.bioconductor.org%2Fgit-version-control.html%23new-package-workflow>

and a FAQ section
http://contributions.bioconductor.org/git-version-control.html#faq<http://secure-web.cisco.com/1R0e7MthE8CqR6G411NYVIS4b_5iHo3Y0twFCWL17QMmeVy3KXEmZ0qTJrF1kpf5dCv44_KBIZ6Vo46MpvbQmODzK8FBZcPhoUqmwRcfCz-1cwYB83CzO6iQApY0HuwkgsSZ_Z0AIhBVSiA2EztAl3IUZ-k__Gzn8DAv85_gZPuQ4aarnDhxCQxXPUUqM_VqP8J2Un5lpOMd5wvMkzvkDF9ZFRtva9QCO0EAgE67wwLLz5kfR-L-DKCC7CizBR0PpanHB1X3NQLSEgt1n-mFrKpujtkrVR3IaNhB5salxLGUHhA_TsQNsHVJunz5CWeXr/http%3A%2F%2Fcontributions.bioconductor.org%2Fgit-version-control.html%23faq>
See especially: #13, #14, and#15





Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Bioc-devel <bioc-devel-bounces using r-project.org<mailto:bioc-devel-bounces using r-project.org>> on behalf of Paul Brennan <brennanpincardiff using gmail.com<mailto:brennanpincardiff using gmail.com>>
Sent: Wednesday, March 6, 2024 9:00 AM
To: bioc-devel using r-project.org<mailto:bioc-devel using r-project.org> <bioc-devel using r-project.org<mailto:bioc-devel using r-project.org>>
Subject: [Bioc-devel] Having problems pushing changes to Bioconductor...

Sorry to bother you I feel as if I am asking a very stupid question but I
can't solve it on my own.

I am getting build errors and I worked out why (a failed test) and changed
my code on Github to correct this:
https://secure-web.cisco.com/1C-fx1Fhx9rZfPJTM0FHB-mLGMfkL6M96AEW9fEr4L0xDKiuAu--2umi29DrHFpl_pWRTIjKBCcIalvMrcKCt2WFZENpLe4QuvKhgBOx9FOmJ1VkGT_u2Tv-bmbWgK1bzBmO2mPC6LF_ZnTpUJjRkDpIsTOP-BtsjhP3a6yGUvmLlwtIfo1lMUD4Gl1ipcUIn7CVHqgGN2GERwAMmnTyqjQtg2yb1035kNIfkRFrK8s40RCrbUytSiymWgBBR8Exk1s3xX51m2KFuuiCSEk9Bhc0bxKl3CUW_V5exgMKWeQS9aGPOCh6NCLMQ6kSbtKPF/https%3A%2F%2Fgithub.com%2Fbrennanpincardiff%2FdrawProteins
I have checked R CMD Check and it is fine with no errors or warnings :-)

Now it is time to try to push these onto Bioconductor but I can't do this.
I've tried various sources and it seems the key point is that I haven't
organised the correct access rights to push upstream.

Can some one advise or point towards a resource that I can work with
please?

Thanks,
Paul

Paul Brennan
package maintainer for drawProteins
https://secure-web.cisco.com/1AJF0ylkW0LYxK_qOGPSaOg0tBDtXraJO8oy5e6dogibE4DF9ygkXszBgGnaEAuTrFGo8tVABQpcGRhBGJi9SSrdtEVRh8gBIMdRVbgktq3CMRZeMflbYC9d5e_qX0SnD0y2A9PnkuC6gdiIW369zhL3MSRmVe0PjaYJGksjmc8O6tGYJo5LVpBjWefmt_eKLvyGwCEaBKxAo6V8iytwL4fjjFWGteiCsqbbIu6j-Hk3P3ABsPR6VryZv0WAqfOAjEpTBtuNxXP3ziZ4lc5nJxjjJLETQ9eerV-4QBseU5jxIACFREUJWt0g3Qzsnw24D/https%3A%2F%2Fbioconductor.org%2Fpackages%2Frelease%2Fbioc%2Fhtml%2FdrawProteins.html
which is giving a build error.

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