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 <iu...@fedoraproject.org> wrote: > 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 > -- 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
