The log of you running configure on your instance allows me to compare it
to the log of when we build it as a package (you don't need to provide that
one).
Honestly, I have no idea right now _why_ pre-built R would fail to move
files to a cifs share when a non-root user can do it. I'm hoping maybe
something will jump out as to how it configures on your setup. We aren't
modifying R's source code at all, nor are we configuring it in a way that
would affect this as far as I know.
Does this also happen with the older R binary RPMs? If you go back to 4.2.3
or 4.2.2, does it happen?
~spot
On Mon, Jun 12, 2023 at 10:38 AM Alexandre Courtiol <
alexandre.court...@gmail.com> wrote:
> "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
>
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