[Bioc-devel] Going "nuclear" with `lfa` and `gcatest` packages

[Kern, Lori]

We are wrapping up some release related tasks.  I will be in touch over the next week about further steps and to coordinate.



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> on behalf of Alex Ochoa, Ph.D. <alejandro.ochoa using duke.edu>
Sent: Friday, April 28, 2023 1:57 PM
To: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: [Bioc-devel] Going "nuclear" with `lfa` and `gcatest` packages

Dear bioc-devel,

It appears I need the "nuclear" option for the `lfa` and `gcatest`
packages, as it was described in the contributor's guide:

https://secure-web.cisco.com/1jvS3acI6XeNG1F7SwJXPNNVufUmXvm4gf2v_1pWiRB-9OFwxix2QYm9m-pzUpIo6YGVD1Bbe8KXhtUp9XAPMAkkdzS42rzvNhyn2dvIvOUJBE8uNpgtV-EHXaVRy9qDxHItgb9SDBg8oEwOQo5QVGqttwUuYEuOs_OX_fDm4XO9EsIpVyMcmFVy1XFNRdQE1ZI-uklUpLZ2VWjODXJjRF6MDeyqKWyMK2xww4Rx2A2xijeo7SgxoS-eDCg7NT2qC8t2WnUWV8XN1dcm8sSSl6IF-IMpQB590Vp9U8InrHWVp0ZtTnYeRw_gRgEeOoyBi/https%3A%2F%2Fcontributions.bioconductor.org%2Fgit-version-control.html%23abandon-changes

I took over `lfa` and `gcatest` internally almost 3 years ago and have
made tons of commits on the GitHub versions since.  However, until last
month I didn't have access to the Bioconductor git versions.  These
Bioconductor versions have always had unrelated histories (starting
back when Bioconductor used SVN); the original maintainer pushed some
updates that were manually reproduced from his GitHub version, but in
general the GitHub versions are the main ones, whereas the
Bioconductor-only updates are reserved to version bumps.  It doesn't
make sense for me to try to merge the two histories, I'd rather
completely overwrite (a la "git push -f") the Bioconductor versions
with the GitHub ones, and maintain them synced from now on.  For `lfa`
I just tried `git push -f upstream devel`, and got the following
expected error:

remote: Resolving deltas: 100% (330/330), done.
remote: FATAL: + refs/heads/devel packages/lfa a.ochoa DENIED by
fallthru
remote: error: hook declined to update refs/heads/devel
To git.bioconductor.org:packages/lfa.git
 ! [remote rejected] devel -> devel (hook declined)
error: failed to push some refs to
'git.bioconductor.org:packages/lfa.git'

The guide says I must contact you to "abandon changes", "start fresh",
"go nuclear", so let me know what to do next!

Thanks!
-Alex


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