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

Hi all,

The admin from our setup created a script that should help you reproduce
our problem (see below).
Of course, it may be that it is not an RPM-related issue, but we hope you
will have an idea on how to solve the issue all the same.

# 1. Prepare VM and set up Samba

- install Fedora 38 Workstation
(Fedora-Workstation-Live-x86_64-38-1.6.iso). Username: 'user'
- disable SELinux (edit /etc/selinux/config and set
"SELINUX=disabled") and
reboot. Alternatively set up SELinux as described here:
https://docs.fedoraproject.org/en-US/quick-docs/samba/

```
sudo dnf install samba
mkdir ~/share
sudo mkdir /mnt/share
sudo smbpasswd -a user
sudo cat << 'EOF' >> /etc/samba/smb.conf
[share]
  path = /home/user/share
  writable = yes
  browsable = yes
  valid users = user
  create mask = 0660
  directory mask = 0770
EOF
sudo systemctl restart smb
sudo mount -t cifs //localhost/share /mnt/share -o username=user,uid=user
```


# 2. Install R with dnf

```
sudo dnf install R
mkdir /mnt/share/R
ln -s /mnt/share/R ~/R
```
- start R and install a package with dependencies (e.g.
"install.packages('dplyr')")
- installation should fail (it does so on our side)


# 3. Compile R from sources

```
sudo dnf erase R
sudo dnf builddep R
sudo dnf install java-17-openjdk-devel
curl -Ls https://cran.r-project.org/src/base/R-4/R-4.3.0.tar.gz | tar xzf -
cd R-4.3.0
./configure
make
sudo make install
```
- installing a package with dependencies should succeed now (on our side at
least)


Many thanks, for having another look at this knot.
Best,
Alex

On Wed, 14 Jun 2023 at 10:50, Alexandre Courtiol <
alexandre.courtiol at gmail.com> wrote:
> 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
>

-- 
Alexandre Courtiol, www.datazoogang.de

	[[alternative HTML version deleted]]

On Thu, 15 Jun 2023 at 00:04, Alexandre Courtiol
<alexandre.courtiol at gmail.com> wrote:
>
> Hi all,
>
> The admin from our setup created a script that should help you reproduce
our problem (see below).
> Of course, it may be that it is not an RPM-related issue, but we hope you
will have an idea on how to solve the issue all the same.
>
> # 1. Prepare VM and set up Samba
>
> - install Fedora 38 Workstation
(Fedora-Workstation-Live-x86_64-38-1.6.iso). Username: 'user'
> - disable SELinux (edit /etc/selinux/config and set
"SELINUX=disabled") and reboot. Alternatively set up SELinux as
described here: https://docs.fedoraproject.org/en-US/quick-docs/samba/
>
> ```
> sudo dnf install samba
> mkdir ~/share
> sudo mkdir /mnt/share
> sudo smbpasswd -a user
> sudo cat << 'EOF' >> /etc/samba/smb.conf
> [share]
>   path = /home/user/share
>   writable = yes
>   browsable = yes
>   valid users = user
>   create mask = 0660
>   directory mask = 0770
> EOF
> sudo systemctl restart smb
> sudo mount -t cifs //localhost/share /mnt/share -o username=user,uid=user
> ```
>
>
> # 2. Install R with dnf
>
> ```
> sudo dnf install R
> mkdir /mnt/share/R
> ln -s /mnt/share/R ~/R
> ```
> - start R and install a package with dependencies (e.g.
"install.packages('dplyr')")
> - installation should fail (it does so on our side)
Well, actually not "a package with dependencies". Only dplyr seems to
fail, but no other package.
> # 3. Compile R from sources
>
> ```
> sudo dnf erase R
> sudo dnf builddep R
> sudo dnf install java-17-openjdk-devel
> curl -Ls https://cran.r-project.org/src/base/R-4/R-4.3.0.tar.gz | tar xzf -
> cd R-4.3.0
> ./configure
> make
> sudo make install
> ```
> - installing a package with dependencies should succeed now (on our side at
least)
The difference with the installation above is that this build is not
installing the help pages. Run R CMD INSTALL with --no-html above and
the installation succeeds too. So something happens with dplyr's html
pages (too many? so too much activity somehow locks the mounted files
temporarily?). No idea, but I don't think it has anything to do with
R.

I?aki
>
>
> Many thanks, for having another look at this knot.
> Best,
> Alex
>
> On Wed, 14 Jun 2023 at 10:50, Alexandre Courtiol <alexandre.courtiol at
gmail.com> wrote:
>>
>> 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
>
>
>
> --
> Alexandre Courtiol, www.datazoogang.de


-- 
I?aki ?car