[R-pkg-devel] Help with a github/Rstudio mess

[Chris Evans]

First, apologies for being off topic.  I guess I can see that this was 
pretty pure git/github/Rstudio with hindsight.  I am very leary of
stackoverflow, probably wrongly, but I find such a mix of misinformation 
and showboating there.  By contrast this list is a haven for me
to learn. However, point taken and I will try to be focused on the R 
package side if I post here again (quite possible as so much of this
is at my outer limits in skills and experience).

So huge thanks to Ivan for so much background: not sure if it's 
depressing or reassuring to see that this seems to be an erratic but known
thing.  Huge thanks to Duncan as I decided that I understood more of his 
suggested fix than of Ivan's so I would start there ... and it
simply worked!

Many thanks both and to all who have taught me so much here,

Chris

On 05/07/2023 10:12, Ivan Krylov wrote:
> On Wed, 5 Jul 2023 09:44:26 +0100
> Chris Evans <chrishold using psyctc.org> wrote:
>
>> OK.  So I try to pull thinking that made sense and that the change to
>> pkgdown.yaml on github that I made yesterday is the offending change.
> You are right about this.
>
>> However, when I pull (in Rstudio again) I get this:
>>
>>   >>> /usr/bin/git pull
>> fatal: pack has 6 unresolved deltas
>> fatal: fetch-pack: invalid index-pack output
> I think it should be possible to get your work online if you push it
> into a separate branch:
>
> git checkout -b test-getCIforQuantiles
> git push -u origin test-getCIforQuantiles
>
> This still leaves the problem of merging it back into "main", but at
> least you'll have a separate copy you'll be able to get back to.
>
> Your clone of the repo seems to have become corrupted somehow. People
> on the Internet mention that this may be related to "shallow" clones
> (made with git clone --depth=...). `git fsck --full` may provide more
> information, but will probably not be able to fix the problem. Removing
> the "origin" remote and adding it back again may fix the problem, or
> not. https://phabricator.wikimedia.org/T46129 is the most informative
> discussion of this problem I could find, and they couldn't solve it
> either.
>
> If you have any other important local branches, push them to GitHub (in
> a similar manner: git push origin LOCAL_BRANCH_NAME:REMOTE_BRANCH_NAME).
> Move your current clone of the repository away and create it anew using
> `git clone`. Once you have merged the branches into appropriate places,
> you will be able to remove them using git branch -d BRANCH_NAME
> (locally) and git push origin :BRANCH_NAME (on GitHub).
>
-- 
Chris Evans (he/him)
Visiting Professor, UDLA, Quito, Ecuador & Honorary Professor, 
University of Roehampton, London, UK.
Work web site: https://www.psyctc.org/psyctc/
CORE site: http://www.coresystemtrust.org.uk/
Personal site: https://www.psyctc.org/pelerinage2016/
E