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 _______________________________________________ R-SIG-Fedora mailing list R-SIG-Fedora@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-fedora
