Re: [R-sig-Fedora] Problem with R, staged installation for packages, and samba share
On Thu, 15 Jun 2023 at 00:04, Alexandre Courtiol
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.
Iñaki
>
>
> Many thanks, for having another look at this knot.
> Best,
> Alex
>
> On Wed, 14 Jun 2023 at 10:50, Alexandre Courtiol
> 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, Iñaki Ucar wrote:
>>>
>>> On Tue, 13 Jun 2023 at 10:35, Alexandre Courtiol
>>> 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 wrote:
>>> >>
>>> >> Update:
>>> >>
>>> >> On Mon, 12 Jun 2023 at 17:40, Iñaki Ucar 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 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
Re: [R-sig-Fedora] 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.court...@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, Iñaki Ucar wrote:
>
>> On Tue, 13 Jun 2023 at 10:35, Alexandre Courtiol
>> 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
>> wrote:
>> >>
>> >> Update:
>> >>
>> >> On Mon, 12 Jun 2023 at 17:40, Iñaki Ucar
>> 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 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.court...@gmail.com> wrote:
>> >> > >>
>> >> > >> "is the staged installation enabled too in the
Re: [R-sig-Fedora] Problem with R, staged installation for packages, and samba share
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, Iñaki Ucar wrote: > On Tue, 13 Jun 2023 at 10:35, Alexandre Courtiol > 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 > wrote: > >> > >> Update: > >> > >> On Mon, 12 Jun 2023 at 17:40, Iñaki Ucar > 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 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.court...@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 > 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.court...@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 < > iu...@fedoraproject.org> wrote: > >> > > > >> > > On Mon, 12 Jun 2023 at 13:19, Tom Callaway > 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, >
