On Tue, 13 Jun 2023 at 10:35, Alexandre Courtiol <alexandre.court...@gmail.com> 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 <iu...@fedoraproject.org> wrote: >> >> Update: >> >> On Mon, 12 Jun 2023 at 17:40, Iñaki Ucar <iu...@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. >> >> 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 <spo...@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.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 <spo...@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.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 <spo...@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. >> > >>>>> >> > >>>>> Iñaki >> > >>>>> >> > >>>>> > >> > >>>>> > ~spot >> > >>>>> > >> > >>>>> > On Mon, Jun 12, 2023, 6:55 AM Alexandre Courtiol < >> > >>>>> > alexandre.court...@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@r-project.org >> > >>>>> > > https://stat.ethz.ch/mailman/listinfo/r-sig-fedora >> > >>>>> > > >> > >>>>> > >> > >>>>> > [[alternative HTML version deleted]] >> > >>>>> > >> > >>>>> > _______________________________________________ >> > >>>>> > R-SIG-Fedora mailing list >> > >>>>> > R-SIG-Fedora@r-project.org >> > >>>>> > https://stat.ethz.ch/mailman/listinfo/r-sig-fedora >> > >>>>> >> > >>>>> >> > >>>>> >> > >>>>> -- >> > >>>>> Iñaki Úcar >> > >>>> >> > >>>> >> > >>>> >> > >>>> -- >> > >>>> Alexandre Courtiol, www.datazoogang.de >> > >> >> > >> >> > >> >> > >> -- >> > >> Alexandre Courtiol, www.datazoogang.de >> > >> > >> > >> > -- >> > Iñaki Úcar >> >> >> >> -- >> Iñaki Úcar > > > > -- > Alexandre Courtiol, www.datazoogang.de -- Iñaki Úcar _______________________________________________ R-SIG-Fedora mailing list R-SIG-Fedora@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-fedora
