[R-sig-Fedora] R.css missing in Fedora R-core rpm

[Iñaki Ucar]

On Wed, 10 Mar 2021 at 12:02, Jeroen Ooms <jeroenooms using gmail.com> wrote:
>
> On Wed, Mar 10, 2021 at 12:18 AM Iñaki Ucar <iucar using fedoraproject.org> wrote:
> >
> > On Tue, 9 Mar 2021 at 23:55, Jeroen Ooms <jeroenooms using gmail.com> wrote:
> > >
> > > On Tue, Mar 9, 2021 at 2:27 PM Iñaki Ucar <iucar using fedoraproject.org> wrote:
> > > >
> > > > On Tue, 9 Mar 2021 at 13:26, Jeroen Ooms <jeroenooms using gmail.com> wrote:
> > > > >
> > > > > When installing an R package from source on Fedora using the standard
> > > > > R-core rpm, we always get a warning at the end because of a missing
> > > > > css file /usr/share/doc/R/html/R.css:
> > > > >
> > > > > ** byte-compile and prepare package for lazy loading
> > > > > ** help
> > > > > *** installing help indices
> > > > > Error in file.copy(file.path(R.home("doc"), "html", "R.css"), outman) :
> > > > >   (converted from warning) problem copying /usr/share/doc/R/html/R.css
> > > > > to /usr/lib64/R/library/00LOCK-systemfonts/00new/systemfonts/html/R.css:
> > > > > No such file or directory
> > > > >
> > > > > But when I try to install the missing file, yum says it is already installed:
> > > > >
> > > > >   yum install /usr/share/doc/R/html/R.css
> > > > >   ## Package R-core-4.0.3-1.fc32.x86_64 is already installed.
> > > > >
> > > > > However it does not actually exist. Perhaps the rpm could make a copy
> > > > > or symlink from /usr/lib64/R/library/base/html/R.css
> > > >
> > > > I assume you are doing this in a docker image. That file is not
> > > > installed because our base images have "tsflags=nodocs" set in
> > > > /etc/dnf/dnf.conf. Unset this before installing R-core, or, even
> > > > better, install packages with --no-docs.
> > >
> > > Perhaps --no-docs should then be the default if tsflags=nodocs? The
> > > default behavior is unfortunate, because it makes install.packages()
> > > fail even if the user is not even interested in documentation, and
> > > people come up with all sorts of workarounds eg:
> > > https://github.com/r-lib/devtools/issues/2084
> >
> > install.packages doesn't fail. devtools does. I see:
> >
> > Warning in file.create(f.tg) :
> >  cannot create file '/usr/share/doc/R/html/packages.html', reason 'No
> > such file or directory'
> > Warning in utils::make.packages.html(.Library, docdir = R.home("doc")) :
> >  cannot update HTML package index
> >
> > The package is correctly installed and usable.
>
> Many systems (including devtools, and many others) are set more strict
> such that installation warnings are turned into errors, to ensure
> users or applications never ends up installing broken packages.

A warning is not an error. I would expect that R raises an error only
when the package is really broken. Otherwise, there's no point in
having warnings and errors. Users have been bitten quite a lot by this
[1], and as a result, the remotes package (which devtools uses)
recently stepped out from this odd default behaviour [2] (not yet
released though).

> Raising this warning by default for every install.packages() is really
> unfortunate default behaviour, especially because it is evidently
> unclear to users why this happens.

About what is unclear to users, I refer again to [1]. But note that
this is *not* default behaviour. It only happens in docker images,
which have this special setting for a special use case, defined in
order to minimize image sizes and enforced by the package manager. It
has nothing to do with the R-core package: it just follows the
official guidelines and marks documentation files as documentation.

I could add some notes about docker in [3]. Note too that there's an
easier way to install CRAN packages in Fedora [4].

[1] https://github.com/r-lib/remotes/issues/403
[2] https://github.com/r-lib/remotes/commit/5a546add30b4538d60d781bc2fa26cd33ccde092
[3] https://cran.r-project.org/bin/linux/fedora/
[4] https://cran.r-project.org/bin/linux/fedora/#additional-packages


--
Iñaki Úcar