"is the staged installation enabled too in the cases you don't see this
issue?"
-> Yes, it should since we stick to default config.
"Can you provide a log of the output (including the commandline with any
options passed) for configure?"
-> If we compile locally there is no issue despite not using any option,
and if we install R from binary, there is no configure log AFAIK, so I am
not sure how to meet this request.
"can you provide the specific mount options for the cifs share?"
->
sec=krb5,multiuser,mfsymlinks,user=smbuser,domain=localdomain,_netdev,noauto,x-systemd.automount
++
On Mon, 12 Jun 2023 at 16:11, Tom Callaway <spo...@gmail.com> wrote:
> 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
>>
>
--
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
