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

On Tue, 13 Jun 2023 at 10:35, Alexandre Courtiol
<alexandre.courtiol at gmail.com> wrote:
>
> Thanks a lot for persevering.
>
> I?aki, 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.

I?aki
>
> Best,
>
> Alex
>
>
>
> On Mon, 12 Jun 2023 at 21:08, I?aki Ucar <iucar at fedoraproject.org>
wrote:
>>
>> Update:
>>
>> On Mon, 12 Jun 2023 at 17:40, I?aki Ucar <iucar at
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.
>>
>> I?aki
>>
>> >
>> > 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
>> >
>> > I?aki
>> >
>> > On Mon, 12 Jun 2023 at 16:48, Tom Callaway <spotrh at
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 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
>> >
>> >
>> >
>> > --
>> > I?aki ?car
>>
>>
>>
>> --
>> I?aki ?car
>
>
>
> --
> Alexandre Courtiol, www.datazoogang.de


--
I?aki ?car

Thanks again, unfortunately it still fails when mounting the drive on a
windows machine (even using nolease) on our end.
We will prepare a fully reproducible example using a virtual machine. This
could take us a day or two.
++

On Tue, 13 Jun 2023 at 11:05, I?aki Ucar <iucar at fedoraproject.org>
wrote:
> On Tue, 13 Jun 2023 at 10:35, Alexandre Courtiol
> <alexandre.courtiol at gmail.com> wrote:
> >
> > Thanks a lot for persevering.
> >
> > I?aki, 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.
>
> I?aki
>
> >
> > Best,
> >
> > Alex
> >
> >
> >
> > On Mon, 12 Jun 2023 at 21:08, I?aki Ucar <iucar at
fedoraproject.org>
> wrote:
> >>
> >> Update:
> >>
> >> On Mon, 12 Jun 2023 at 17:40, I?aki Ucar <iucar at
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.
> >>
> >> I?aki
> >>
> >> >
> >> > 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
> >> >
> >> > I?aki
> >> >
> >> > On Mon, 12 Jun 2023 at 16:48, Tom Callaway <spotrh at
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 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
> >> >
> >> >
> >> >
> >> > --
> >> > I?aki ?car
> >>
> >>
> >>
> >> --
> >> I?aki ?car
> >
> >
> >
> > --
> > Alexandre Courtiol, www.datazoogang.de
>
>
>
> --
> I?aki ?car
>

-- 
Alexandre Courtiol, www.datazoogang.de

	[[alternative HTML version deleted]]