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

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

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?
(and yes, I am aware of your excellent cran2copr
<https://copr.fedorainfracloud.org/coprs/iucar/cran/> project).

Tom, yes it also created the same issue with older RPMs. Please also find
the configure log attached to this email.

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

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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