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