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

Kern, Lori Lor|@Shepherd @end|ng |rom Ro@we||P@rk@org
Tue May 2 13:58:29 CEST 2023

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:


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
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

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


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