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

[Chris Evans]

I hope this is a legitimate question here.  I have a package of very 
simple functions: https://github.com/cpsyctc/CECPfuns.  For the forseeable
future it's really only to stop me constantly having to rewrite 
functions I use and it is only also used by probably two or three 
colleagues who
also use R and are even less IT/programming/R competent than I am and 
are very happy to use my functions.

I hadn't done any work on it for two years but came back to it yesterday 
and added a function (getCIforQuantiles).  There were warnings about
things that are deprecated now in some of the older functions but 
otherwise things seemed OK.  However, I got a pkgdown error and warning 
after
pushing the updated package to github:

Annotations
1 error and 1 warning
pkgdown
Failed to get R 4.3.1: Failed to get R 4.3.1: Failed to download version 
4.3.1: Error: Unexpected HTTP response: 404
r-lib/actions/setup-r using v1 is deprecated.
r-lib/actions/setup-r using v1 is deprecated. Please update your workflow to 
use the 'v2' version. Also look at the examples at 
https://github.com/r-lib/actions/tree/v2/examples because '@v2' 
workflows are much simpler than 'v1' workflows.

So I tweaked 
https://github.com/cpsyctc/CECPfuns/blob/main/.github/workflows/pkgdown.yaml 
to change
    - uses: r-lib/actions/setup-r using v1
to
    - uses: r-lib/actions/setup-r using v2
rather optimistically hoping that might make the warning go away.

Today I did some work on the new function (trivial, correcting one 
"!is.na(" to the correct "is.na(" !!!).  More importantly, I created the
test-getCIforQuantiles.R file for testthat to test the sanity checks and 
add three simple output checks.

I built the source package locally, committed the changes and tried to 
push the update to github (inside Rstudio) but I get:

 >>> /usr/bin/git push origin HEAD:refs/heads/main
To https://github.com/cpsyctc/CECPfuns.git
  ! [rejected]        HEAD -> main (fetch first)
error: failed to push some refs to 'https://github.com/cpsyctc/CECPfuns.git'
hint: Updates were rejected because the remote contains work that you do
hint: not have locally. This is usually caused by another repository pushing
hint: to the same ref. You may want to first integrate the remote changes
hint: (e.g., 'git pull ...') before pushing again.
hint: See the 'Note about fast-forwards' in 'git push --help' for details.

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.

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 have never felt on top of the complexities of git and github but I'm 
clearly way out of my depth.  I am hoping someone here can see what
I need to do to get things back in synch and be able to get back to 
developing the package.

TIA,

Chris

-- 
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/