Thanks for the tip but nope: SELinux is off on that system...
On Mon, 12 Jun 2023 at 13:24, Iñaki Ucar <iu...@fedoraproject.org> wrote:
> On Mon, 12 Jun 2023 at 13:19, Tom Callaway <spo...@gmail.com> wrote:
> >
> > Hmm, that's a weird one. Is SELinux on and enforcing on that setup?
>
> I was going to bet on the same thing. :) But let me add: if the answer
> is affirmative, and this doesn't happen with SELinux disabled, then
> *the answer is NOT to disable SELinux*. Instead, let's figure this
> out, because the answer is to set the proper labels or permissions.
>
> Iñaki
>
> >
> > ~spot
> >
> > On Mon, Jun 12, 2023, 6:55 AM Alexandre Courtiol <
> > alexandre.court...@gmail.com> wrote:
> >
> > > Dear Fedora-R enthusiasts,
> > >
> > > We are experiencing some issues with the binary releases of R 4.3 for
> > > Fedora 37 & 38 when running it on our infrastructure.
> > >
> > > The issue is that packages won't install, unless the (default) staged
> > > installation process for packages is switched off
> (--no-staged-install).
> > >
> > > It seems to be related to the fact that we are storing R libraries on a
> > > drive mounted via samba share.
> > >
> > > Interestingly, installing R from sources does not cause the issue.
> > > When using other OS (e.g. Arch) on the same infrastructure, the problem
> > > also disappears.
> > >
> > > We are looking for a way out that would allow users to install R
> packages
> > > as usual and that would ideally not force the admin to install R from
> > > sources.
> > >
> > > The issue should be reproducible as follows:
> > >
> > > 1. Mount the share:
> > >
> > > $ mount -t cifs //server/share /mnt/share -o ...options...
> > >
> > > 2. Put R library onto the share:
> > >
> > > $ mkdir /mnt/share/R
> > > $ ln -s /mnt/share/R ~/R
> > >
> > > 3. Install a package that has dependencies (It doesn't matter whether
> the
> > > dependencies actually have to be installed or not. E.g. if you install
> all
> > > of the dependencies of 'dplyr' and then install 'dplyr' itself in an
> extra
> > > call to 'install.packages', the problem will still be triggered.):
> > >
> > > $ Rscript -e "install.packages('dplyr', repos='
> https://cloud.r-project.org
> > > ')"
> > >
> > > 4. The installation will fail while trying to move the package to its
> final
> > > location:
> > >
> > > mv: cannot move
> > >
> '/mnt/share/R/x86_64-redhat-linux-gnu-library/4.3/00LOCK-dplyr/00new/dplyr'
> > > to '/mnt/share/R/x86_64-redhat-linux-gnu-library/4.3/dplyr': Permission
> > > denied
> > > ERROR: moving to final location failed
> > >
> > > 5. Moving the folder as described in the error manually from the shell
> > > succeeds:
> > >
> > > $ mv
> > >
> /mnt/share/R/x86_64-redhat-linux-gnu-library/4.3/00LOCK-dplyr/00new/dplyr
> > > /mnt/share/R/x86_64-redhat-linux-gnu-library/4.3/dplyr
> > > $ # => works
> > >
> > > And if R is either compiled from source (taking the usual
> > > "configure/make/make install" route) or installed from Conda, the
> > > permission error at step 4 doesn't happen. We also tested creating the
> > > binary RPM package on the same machine, and the result was the same as
> > > installing the binary package from the repo (i.e. error).
> > >
> > > ++
> > >
> > >
> > > --
> > > Alexandre Courtiol, www.datazoogang.de
> > >
> > > [[alternative HTML version deleted]]
> > >
> > > _______________________________________________
> > > R-SIG-Fedora mailing list
> > > R-SIG-Fedora@r-project.org
> > > https://stat.ethz.ch/mailman/listinfo/r-sig-fedora
> > >
> >
> > [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > R-SIG-Fedora mailing list
> > R-SIG-Fedora@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-fedora
>
>
>
> --
> Iñaki Úcar
>
--
Alexandre Courtiol, www.datazoogang.de
[[alternative HTML version deleted]]
_______________________________________________
R-SIG-Fedora mailing list
R-SIG-Fedora@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-fedora
