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 <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 > -- 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
