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

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 at gmail.com> wrote:
> Thanks for the tip but nope: SELinux is off on that system...
>
> On Mon, 12 Jun 2023 at 13:24, I?aki Ucar <iucar at fedoraproject.org>
wrote:
>
>> On Mon, 12 Jun 2023 at 13:19, Tom Callaway <spotrh at 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.
>>
>> I?aki
>>
>> >
>> > ~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
>> > >
>> >
>> >         [[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
>>
>>
>>
>> --
>> I?aki ?car
>>
>
>
> --
> Alexandre Courtiol, www.datazoogang.de
>
	[[alternative HTML version deleted]]

"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 at 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 at gmail.com> wrote:
>
>> Thanks for the tip but nope: SELinux is off on that system...
>>
>> On Mon, 12 Jun 2023 at 13:24, I?aki Ucar <iucar at
fedoraproject.org> wrote:
>>
>>> On Mon, 12 Jun 2023 at 13:19, Tom Callaway <spotrh at
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.
>>>
>>> I?aki
>>>
>>> >
>>> > ~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
>>> > >
>>> >
>>> >         [[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
>>>
>>>
>>>
>>> --
>>> I?aki ?car
>>>
>>
>>
>> --
>> Alexandre Courtiol, www.datazoogang.de
>>
>
-- 
Alexandre Courtiol, www.datazoogang.de

	[[alternative HTML version deleted]]

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 at 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 at 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 at gmail.com> wrote:
>>
>>> Thanks for the tip but nope: SELinux is off on that system...
>>>
>>> On Mon, 12 Jun 2023 at 13:24, I?aki Ucar <iucar at
fedoraproject.org>
>>> wrote:
>>>
>>>> On Mon, 12 Jun 2023 at 13:19, Tom Callaway <spotrh at
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.
>>>>
>>>> I?aki
>>>>
>>>> >
>>>> > ~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
>>>> > >
>>>> >
>>>> >         [[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
>>>>
>>>>
>>>>
>>>> --
>>>> I?aki ?car
>>>>
>>>
>>>
>>> --
>>> Alexandre Courtiol, www.datazoogang.de
>>>
>>
>
> --
> Alexandre Courtiol, www.datazoogang.de
>
	[[alternative HTML version deleted]]