1. I ran ```rpm --rebuilddb``` to check the problem wasn't something corrupted in there.

2. I had run ```dnf clean all``` shortly before this, so there should be no contribution from corrupted files in /var/cache/dnf.

3. The problem persists after a ```dnf reinstall``` of both xstatic-jquery-ui-common and R-shiny.

I briefly looked into it and it looks like:

1. R-shiny-1.5.0-1.fc33~bootstrap.noarch used to have dependency on xstatic-jquery-ui-common
2. during the installation R-shide does "unbundling things" - in this case replacing /usr/share/R/library/shiny/www/shared/jqueryui with a symlink to /usr/share/javascript/jquery_ui
3. the xstatic-jquery-ui-common requirement has been dropped in R-shiny-1.5.0-3.fc33~bootstrap.noarch

So R-shine is trying to replace a symlink with directory during upgrade from version 1.5.0-1 to 1.5.0-3 which is complicated - see https://docs.fedoraproject.org/en-US/packaging-guidelines/Directory_Replacement/

I'm going to re-assign the issue to R-shine to deal with the problem. As a workaround - removal of the xstatic-jquery-ui-common and R-shiny packages and installing R-shiny-1.5.0-3.fc33~bootstrap.noarch from updates repo should work.

Yes, I worked around it by removing the package then installing the new version (along with all the packages that depend on it :)).

The document solution (pre-trans lua scriptlet) should work fine.

I'm sorry, I have no idea how to fix this.

I followed the Directory replacement guidelines, and added the following scriptlet:

# Necessary to re-bundle jQuery UI, which was in an orphaned package. The
# symlink must be explicitly deleted to become a directory.
%pretrans -p <lua> -n R-%{packname}
path = "%{rlibdir}/%{packname}/www/shared/jqueryui"
st = posix.stat(path)
print(path)
print(st)
print(st.type)
if st and st.type == "link" then
  os.remove(path)
end

and I can see it is attached to the rpm:

$ rpm -q --scripts -p ./R-shiny-1.5.0-4.fc33~bootstrap.noarch.rpm
pretrans scriptlet (using <lua>):
path = "/usr/share/R/library/shiny/www/shared/jqueryui"
st = posix.stat(path)
print(path)
print(st)
print(st.type)
if st and st.type == "link" then
  os.remove(path)
end

but when I run it in mock, the scriptlet does not trigger before the transaction:

Dependencies resolved:
=======================================================================================================================================
 Package                            Architecture            Version                 Repository               Size
=======================================================================================================================================
Upgrading:
 R-shiny                            noarch                  1.5.0-4.fc33~bootstrap  @commandline             4.2 M

Transaction Summary
=======================================================================================================================================
Upgrade  1 Package

Total size: 4.2 M
Downloading Packages:
Running transaction check
Transaction check succeeded.
Running transaction test
Error: Transaction test error:
  file /usr/share/R/library/shiny/www/shared/jqueryui/images/ui-icons_444444_256x240.png from install of R-shiny-1.5.0-4.fc33~bootstrap.noarch conflicts with file from package xstatic-jquery-ui-common-1.12.0.1-12.fc33.noarch
  file /usr/share/R/library/shiny/www/shared/jqueryui/images/ui-icons_555555_256x240.png from install of R-shiny-1.5.0-4.fc33~bootstrap.noarch conflicts with file from package xstatic-jquery-ui-common-1.12.0.1-12.fc33.noarch
  file /usr/share/R/library/shiny/www/shared/jqueryui/images/ui-icons_777620_256x240.png from install of R-shiny-1.5.0-4.fc33~bootstrap.noarch conflicts with file from package xstatic-jquery-ui-common-1.12.0.1-12.fc33.noarch
  file /usr/share/R/library/shiny/www/shared/jqueryui/images/ui-icons_777777_256x240.png from install of R-shiny-1.5.0-4.fc33~bootstrap.noarch conflicts with file from package xstatic-jquery-ui-common-1.12.0.1-12.fc33.noarch
  file /usr/share/R/library/shiny/www/shared/jqueryui/images/ui-icons_cc0000_256x240.png from install of R-shiny-1.5.0-4.fc33~bootstrap.noarch conflicts with file from package xstatic-jquery-ui-common-1.12.0.1-12.fc33.noarch
  file /usr/share/R/library/shiny/www/shared/jqueryui/images/ui-icons_ffffff_256x240.png from install of R-shiny-1.5.0-4.fc33~bootstrap.noarch conflicts with file from package xstatic-jquery-ui-common-1.12.0.1-12.fc33.noarch
  file /usr/share/R/library/shiny/www/shared/jqueryui/jquery-ui.css from install of R-shiny-1.5.0-4.fc33~bootstrap.noarch conflicts with file from package xstatic-jquery-ui-common-1.12.0.1-12.fc33.noarch
  file /usr/share/R/library/shiny/www/shared/jqueryui/jquery-ui.js from install of R-shiny-1.5.0-4.fc33~bootstrap.noarch conflicts with file from package xstatic-jquery-ui-common-1.12.0.1-12.fc33.noarch
  file /usr/share/R/library/shiny/www/shared/jqueryui/jquery-ui.min.css from install of R-shiny-1.5.0-4.fc33~bootstrap.noarch conflicts with file from package xstatic-jquery-ui-common-1.12.0.1-12.fc33.noarch
  file /usr/share/R/library/shiny/www/shared/jqueryui/jquery-ui.min.js from install of R-shiny-1.5.0-4.fc33~bootstrap.noarch conflicts with file from package xstatic-jquery-ui-common-1.12.0.1-12.fc33.noarch
  file /usr/share/R/library/shiny/www/shared/jqueryui/jquery-ui.structure.css from install of R-shiny-1.5.0-4.fc33~bootstrap.noarch conflicts with file from package xstatic-jquery-ui-common-1.12.0.1-12.fc33.noarch
  file /usr/share/R/library/shiny/www/shared/jqueryui/jquery-ui.structure.min.css from install of R-shiny-1.5.0-4.fc33~bootstrap.noarch conflicts with file from package xstatic-jquery-ui-common-1.12.0.1-12.fc33.noarch
  file /usr/share/R/library/shiny/www/shared/jqueryui/jquery-ui.theme.css from install of R-shiny-1.5.0-4.fc33~bootstrap.noarch conflicts with file from package xstatic-jquery-ui-common-1.12.0.1-12.fc33.noarch
  file /usr/share/R/library/shiny/www/shared/jqueryui/jquery-ui.theme.min.css from install of R-shiny-1.5.0-4.fc33~bootstrap.noarch conflicts with file from package xstatic-jquery-ui-common-1.12.0.1-12.fc33.noarch

I think you should distinct between Fedora 33 and Fedora 34.

On Fedora 34, package python-XStatic-jquery-ui is orphaned and is not found in the repositories. So there should be no conflicts.

On Fedora 33, package xstatic-jquery-ui-common-1.12.0.1-12.fc33.noarch is in the release repository. It may be installed on Fedora 33 systems, and it is still installable.

I think, a solution might be to distinguish in the spec file whether building for Fedora 33 or Fedora 34 (with an if-then-else condition).
If the package is to be built for Fedora 33 or before, then the old code from R-shiny-1.5.0-1.fc33~bootstrap should be active in the spec file.
If the package is to be built for Fedora 34 or newer, then the new code from R-shiny-1.5.0-3.fc33~bootstrap should be active in the spec file.

You can do this by creating an update to R-shiny (e.g. version 1.5.0-4). Fedora 34 will get a new package, which contains the same files as the package before. Fedora 33 is effectively reverted to version 1.5.0-1 but with a higher version number.

%if (0%{?fedora} && 0%{?fedora} < 34)
... (old part)
%else
... (new part)
%endif

Unfortunately, I don't think that will help. If 1.5.0-3.fc33 -> 1.5.0-4.fc33 switches directories to symlinks, then I need a scriptlet to do that for people who installed -3, but that seems to be broken. And then for F34, I'll need to add the symlink->directory scriptlet, or that upgrade will not work. So some part of the upgrade will be broken somewhere.

I believe this is actually a problem in rpm itself, see bug 1936422.

FEDORA-2021-dc90973959 has been submitted as an update to Fedora 34. https://bodhi.fedoraproject.org/updates/FEDORA-2021-dc90973959

FEDORA-2021-dc90973959 has been pushed to the Fedora 34 testing repository.
Soon you'll be able to install the update with the following command:
`sudo dnf upgrade --enablerepo=updates-testing --advisory=FEDORA-2021-dc90973959`
You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2021-dc90973959

See also https://fedoraproject.org/wiki/QA:Updates_Testing for more information on how to test updates.

FEDORA-2021-dc90973959 has been pushed to the Fedora 34 stable repository.
If problem still persists, please make note of it in this bug report.