Okay, so if it's not SELinux... perhaps something about how R is being
configured is different?
Can you provide a log of the output (including the commandline with any
options passed) for configure?
Also, can you provide the specific mount options for the cifs share?
~spot
On Mon, Jun 12, 2023 at 9:12 AM Alexandre Courtiol <
alexandre.court...@gmail.com> wrote:
> 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
>
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