R SIG Fedora - Jun 2023 - Problem with R, staged installation for packages, and samba share

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

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Hmm, that's a weird one. Is SELinux on and enforcing on that setup?

~spot

On Mon, Jun 12, 2023, 6:55 AM Alexandre Courtiol <
alexandre.courtiol at 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 at r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-fedora
>
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