[R-sig-Fedora] Problem with R, staged installation for packages, and samba share

Iñaki Ucar |uc@r @end|ng |rom |edor@project@org
Tue Jun 13 11:05:38 CEST 2023 

On Tue, 13 Jun 2023 at 10:35, Alexandre Courtiol
<alexandre.courtiol using gmail.com> wrote:
>
> Thanks a lot for persevering.
>
> Iñaki, that sounds very promising, could you please tell me what software your SMB share is running on (i.e. what does the server side look like?), and if it's Samba, then what version did you use?

There was a Windows 10 machine around, so I created a test folder and
hit "share".

> (and yes, I am aware of your excellent cran2copr project).
>
> Tom, yes it also created the same issue with older RPMs. Please also find the configure log attached to this email.

I see no significant differences, so this supports the hypothesis that
the issue is in the mount.

Iñaki

>
> Best,
>
> Alex
>
>
>
> On Mon, 12 Jun 2023 at 21:08, Iñaki Ucar <iucar using fedoraproject.org> wrote:
>>
>> Update:
>>
>> On Mon, 12 Jun 2023 at 17:40, Iñaki Ucar <iucar using fedoraproject.org> wrote:
>> >
>> > Unfortunately, I cannot reproduce the issue here. :( I mounted a smb
>> > share, created a symlink from ~/R, and installed dplyr without any
>> > issue (apart from the installation process taking ages). Fortunately,
>> > this rules out our binary R package as responsible for the issue you
>> > are experiencing, unless I'm missing something.
>>
>> The experiment above was done using kio-fuse to mount the folder. Now
>> I've been able to reproduce the error using a regular CIFS mount. I
>> reproduced this both with Fedora and Debian R binaries. Then I
>> executed the installation step by step, and I checked that, when the
>> mv command is invoked, manually running mv in the console does trigger
>> the error too. So again, I don't think there's any issue with R.
>>
>> However, I've also managed to fix the issue by adding the nolease
>> option to the mount command. Hope it helps.
>>
>> Iñaki
>>
>> >
>> > Issue aside, may I ask what is the purpose of putting the library in a
>> > smb share? May I suggest [1]?
>> >
>> > [1] https://cran.r-project.org/bin/linux/fedora/#additional-packages
>> >
>> > Iñaki
>> >
>> > On Mon, 12 Jun 2023 at 16:48, Tom Callaway <spotrh using gmail.com> wrote:
>> > >
>> > > 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.courtiol using 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 <spotrh using 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.courtiol using 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 <iucar using fedoraproject.org> wrote:
>> > >>>>>
>> > >>>>> On Mon, 12 Jun 2023 at 13:19, Tom Callaway <spotrh using 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.courtiol using 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 using r-project.org
>> > >>>>> > > https://stat.ethz.ch/mailman/listinfo/r-sig-fedora
>> > >>>>> > >
>> > >>>>> >
>> > >>>>> >         [[alternative HTML version deleted]]
>> > >>>>> >
>> > >>>>> > _______________________________________________
>> > >>>>> > R-SIG-Fedora mailing list
>> > >>>>> > R-SIG-Fedora using r-project.org
>> > >>>>> > https://stat.ethz.ch/mailman/listinfo/r-sig-fedora
>> > >>>>>
>> > >>>>>
>> > >>>>>
>> > >>>>> --
>> > >>>>> Iñaki Úcar
>> > >>>>
>> > >>>>
>> > >>>>
>> > >>>> --
>> > >>>> Alexandre Courtiol, www.datazoogang.de
>> > >>
>> > >>
>> > >>
>> > >> --
>> > >> Alexandre Courtiol, www.datazoogang.de
>> >
>> >
>> >
>> > --
>> > Iñaki Úcar
>>
>>
>>
>> --
>> Iñaki Úcar
>
>
>
> --
> Alexandre Courtiol, www.datazoogang.de



--
Iñaki Úcar

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