Thanks a lot Iñaki for narrowing down the problem. That is definitely an important insight that might bring us forward.
++ On Thu, 15 Jun 2023 at 02:28, Iñaki Ucar <iu...@fedoraproject.org> wrote: > 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 > -- 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
