On Thu, 15 Jun 2023 at 00:04, Alexandre Courtiol <alexandre.court...@gmail.com> wrote: > > 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)
Well, actually not "a package with dependencies". Only dplyr seems to fail, but no other package. > # 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) The difference with the installation above is that this build is not installing the help pages. Run R CMD INSTALL with --no-html above and the installation succeeds too. So something happens with dplyr's html pages (too many? so too much activity somehow locks the mounted files temporarily?). No idea, but I don't think it has anything to do with R. Iñaki > > > 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 -- Iñaki Úcar _______________________________________________ R-SIG-Fedora mailing list R-SIG-Fedora@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-fedora
