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?
(and yes, I am aware of your excellent cran2copr
<https://copr.fedorainfracloud.org/coprs/iucar/cran/> project).
Tom, yes it also created the same issue with older RPMs. Please also find
the configure log attached to this email.
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
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checking whether ftell works correctly on files opened for append... yes
checking for working sigaction... yes
checking whether mktime, gmtime, localtime work correctly in 2020... yes
checking whether mktime sets errno... no
checking whether mktime works correctly after 2037... yes
checking whether mktime works correctly before 1902... yes
checking whether mktime works correctly in 1969... yes
checking for complex.h... yes
checking for double complex... yes
checking whether C99 double complex is supported... yes
checking whether cabs exists and is declared... yes
checking whether carg exists and is declared... yes
checking whether cexp exists and is declared... yes
checking whether clog exists and is declared... yes
checking whether csqrt exists and is declared... yes
checking whether cpow exists and is declared... yes
checking whether ccos exists and is declared... yes
checking whether csin exists and is declared... yes
checking whether ctan exists and is declared... yes
checking whether cacos exists and is declared... yes
checking whether casin exists and is declared... yes
checking whether catan exists and is declared... yes
checking whether ccosh exists and is declared... yes
checking whether csinh exists and is declared... yes
checking whether ctanh exists and is declared... yes
checking for working ctanh... yes
checking whether 'struct tm' includes tm_zone... yes
checking whether 'struct tm' includes tm_gmtoff... yes
checking for dgemm_ in -llapack... no
checking for dpstrf_ in -llapack... no
checking if LAPACK version >= 3.10.0... no
configure: using internal LAPACK sources
checking for iconv.h... yes
checking for iconv... yes
checking whether iconv accepts "UTF-8", "latin1", "ASCII" and "UCS-*"... yes
checking whether iconv accepts "CP1252"... yes
checking for iconvlist... no
checking for iconv... yes
checking for iconv declaration...
extern size_t iconv (iconv_t cd, char * *inbuf, size_t *inbytesleft, char * *outbuf, size_t *outbytesleft);
checking for wchar.h... (cached) yes
checking for wctype.h... yes
checking whether mbrtowc exists and is declared... yes
checking whether wcrtomb exists and is declared... yes
checking whether wcscoll exists and is declared... yes
checking whether wcsftime exists and is declared... yes
checking whether wcstod exists and is declared... yes
checking whether mbstowcs exists and is declared... yes
checking whether wcstombs exists and is declared... yes
checking whether wctrans exists and is declared... yes
checking whether wctype exists and is declared... yes
checking whether iswctype exists and is declared... yes
checking whether wcwidth exists and is declared... yes
checking whether wcswidth exists and is declared... yes
checking for wctrans_t... yes
checking for mbstate_t... yes
checking for ICU... yes
checking for X... libraries , headers
checking for gethostbyname... yes
checking for connect... yes
checking for remove... yes
checking for shmat... yes
checking for IceConnectionNumber in -lICE... yes
checking for X11/Intrinsic.h... yes
checking for XtToolkitInitialize in -lXt... yes
using X11 ... yes
checking for KeySym... yes
checking for X11/Xmu/Atoms.h... yes
checking for XmuInternAtom in -lXmu... yes
checking whether pkg-config knows about cairo and pango... yes
checking whether cairo including pango is >= 1.2 and works... yes
checking for tclConfig.sh... no
checking for tclConfig.sh in library (sub)directories... /usr/lib64/tclConfig.sh
checking for tkConfig.sh... no
checking for tkConfig.sh in library (sub)directories... /usr/lib64/tkConfig.sh
checking for tcl.h... yes
checking for tk.h... yes
checking whether compiling/linking Tcl/Tk code works... yes
checking for BSD networking... yes
checking for rpc/types.h... no
checking for tirpc/rpc/types.h... yes
checking for tirpc/rpc/xdr.h... yes
checking for XDR support... yes
checking for inflateInit2_ in -lz... yes
checking for zlib.h... yes
checking if zlib version >= 1.2.5... yes
checking whether zlib support suffices... yes
checking for BZ2_bzlibVersion in -lbz2... yes
checking for bzlib.h... yes
checking if bzip2 version >= 1.0.6... yes
checking whether bzip2 support suffices... yes
checking for lzma_version_number in -llzma... yes
checking for lzma.h... yes
checking if lzma version >= 5.0.3... yes
checking for pcre2.h... yes
checking for pcre2_compile_8 in -lpcre2-8... yes
checking if PCRE2 has Unicode support... yes
checking whether PCRE support suffices... yes
checking for curl-config... /usr/bin/curl-config
checking libcurl version ... 8.0.1
checking for curl/curl.h... yes
checking if libcurl is >= 7.28.0... yes
checking if libcurl supports https... yes
checking if pkg-config knows about libjpeg... yes
checking if jpeglib version >= 6b... yes
checking for jpeg_destroy_compress in -ljpeg... yes
checking if pkg-config knows about libpng... yes
checking if libpng version >= 1.2.7... yes
checking for png_create_write_struct in -lpng... yes
checking if pkg-config knows about libtiff... yes
checking for tiffio.h... yes
checking for TIFFOpen in -ltiff... yes
checking whether leap seconds are treated according to POSIX... yes
checking for inline... inline
checking for struct stat.st_atim.tv_nsec... yes
checking whether struct stat.st_atim is of type struct timespec... yes
checking for setitimer... yes
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking for _LARGEFILE_SOURCE value needed for large files... no
checking whether KERN_USRSTACK sysctl is supported... no
checking for visible __lib_stack_end... yes
checking for lpr... lpr
checking for paperconf... false
checking for Fortran flag to compile .f90 files... none
checking for Fortran flag to compile .f95 files... none
checking for gfortran option to support OpenMP... (cached) -fopenmp
checking for recommended packages... yes
checking whether NLS is requested... yes
Configuring src/extra/intl directory
checking for a race-free mkdir -p... /usr/bin/mkdir -p
checking whether we are using the GNU C Library 2 or newer... yes
checking for ranlib... (cached) ranlib
checking for simple visibility declarations... yes
checking for stdint.h... yes
checking for getpagesize... yes
checking for working mmap... yes
checking whether integer division by zero raises SIGFPE... no
checking for inttypes.h... yes
checking for unsigned long long int... yes
checking for inttypes.h... (cached) yes
checking whether the inttypes.h PRIxNN macros are broken... no
checking for ld used by gcc... /usr/bin/ld -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
checking for shared library run path origin... done
checking whether imported symbols can be declared weak... yes
checking for multithread API to use... none
checking for argz.h... yes
checking for inttypes.h... (cached) yes
checking for limits.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... (cached) yes
checking for getcwd... yes
checking for getegid... yes
checking for geteuid... yes
checking for getgid... yes
checking for getuid... yes
checking for mempcpy... (cached) yes
checking for munmap... yes
checking for stpcpy... yes
checking for strcasecmp... yes
checking for strdup... (cached) yes
checking for strtoul... yes
checking for tsearch... yes
checking for argz_count... yes
checking for argz_stringify... yes
checking for argz_next... yes
checking for __fsetlocking... yes
checking whether feof_unlocked is declared... yes
checking whether fgets_unlocked is declared... yes
checking for iconv... (cached) yes
checking for iconv declaration... (cached)
extern size_t iconv (iconv_t cd, char * *inbuf, size_t *inbytesleft, char * *outbuf, size_t *outbytesleft);
checking for NL_LOCALE_NAME macro... yes
checking for bison... no
checking for long long int... yes
checking for long double... yes
checking for wchar_t... yes
checking for wint_t... yes
checking for intmax_t... yes
checking whether printf() supports POSIX/XSI format strings... yes
checking whether we are using the GNU C Library 2.1 or newer... yes
checking for stdint.h... (cached) yes
checking for SIZE_MAX... yes
checking for stdint.h... (cached) yes
checking for CFPreferencesCopyAppValue... no
checking for CFLocaleCopyCurrent... no
checking for ptrdiff_t... yes
checking for stddef.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for asprintf... yes
checking for fwprintf... yes
checking for putenv... (cached) yes
checking for setenv... yes
checking for setlocale... yes
checking for snprintf... yes
checking for wcslen... yes
checking whether _snprintf is declared... no
checking whether _snwprintf is declared... no
checking whether getc_unlocked is declared... yes
checking for nl_langinfo and CODESET... (cached) yes
checking for LC_MESSAGES... yes
checking for CFPreferencesCopyAppValue... (cached) no
checking for CFLocaleCopyCurrent... (cached) no
checking whether included gettext is requested... no
checking for GNU gettext in libc... yes
checking whether to use NLS... yes
checking where the gettext function comes from... libc
Finished configuring src/extra/intl directory
checking whether OpenMP SIMD reduction is supported... yes
using as R_SHELL for scripts ... /bin/sh
configure: creating ./config.status
config.status: creating Makeconf
config.status: creating Makefile
config.status: creating doc/Makefile
config.status: creating doc/html/Makefile
config.status: creating doc/manual/Makefile
config.status: creating etc/Makefile
config.status: creating etc/Makeconf
config.status: creating etc/Renviron
config.status: creating etc/javaconf
config.status: creating etc/ldpaths
config.status: creating m4/Makefile
config.status: creating po/Makefile
config.status: creating share/Makefile
config.status: creating src/Makefile
config.status: creating src/appl/Makefile
config.status: creating src/extra/Makefile
config.status: creating src/extra/blas/Makefile
config.status: creating src/extra/intl/Makefile
config.status: creating src/extra/tre/Makefile
config.status: creating src/extra/tzone/Makefile
config.status: creating src/extra/xdr/Makefile
config.status: creating src/include/Makefile
config.status: creating src/include/Rmath.h0
config.status: creating src/include/R_ext/Makefile
config.status: creating src/library/Recommended/Makefile
config.status: creating src/library/Makefile
config.status: creating src/library/base/DESCRIPTION
config.status: creating src/library/base/Makefile
config.status: creating src/library/compiler/DESCRIPTION
config.status: creating src/library/compiler/Makefile
config.status: creating src/library/datasets/DESCRIPTION
config.status: creating src/library/datasets/Makefile
config.status: creating src/library/graphics/DESCRIPTION
config.status: creating src/library/graphics/Makefile
config.status: creating src/library/graphics/src/Makefile
config.status: creating src/library/grDevices/DESCRIPTION
config.status: creating src/library/grDevices/Makefile
config.status: creating src/library/grDevices/src/Makefile
config.status: creating src/library/grDevices/src/cairo/Makefile
config.status: creating src/library/grid/DESCRIPTION
config.status: creating src/library/grid/Makefile
config.status: creating src/library/grid/src/Makefile
config.status: creating src/library/methods/DESCRIPTION
config.status: creating src/library/methods/Makefile
config.status: creating src/library/methods/src/Makefile
config.status: creating src/library/parallel/DESCRIPTION
config.status: creating src/library/parallel/Makefile
config.status: creating src/library/parallel/src/Makefile
config.status: creating src/library/profile/Makefile
config.status: creating src/library/stats/DESCRIPTION
config.status: creating src/library/stats/Makefile
config.status: creating src/library/stats/src/Makefile
config.status: creating src/library/stats4/DESCRIPTION
config.status: creating src/library/stats4/Makefile
config.status: creating src/library/splines/DESCRIPTION
config.status: creating src/library/splines/Makefile
config.status: creating src/library/splines/src/Makefile
config.status: creating src/library/tcltk/DESCRIPTION
config.status: creating src/library/tcltk/Makefile
config.status: creating src/library/tcltk/src/Makefile
config.status: creating src/library/tools/DESCRIPTION
config.status: creating src/library/tools/Makefile
config.status: creating src/library/tools/src/Makefile
config.status: creating src/library/translations/DESCRIPTION
config.status: creating src/library/translations/Makefile
config.status: creating src/library/utils/DESCRIPTION
config.status: creating src/library/utils/Makefile
config.status: creating src/library/utils/src/Makefile
config.status: creating src/main/Makefile
config.status: creating src/modules/Makefile
config.status: creating src/modules/X11/Makefile
config.status: creating src/modules/internet/Makefile
config.status: creating src/modules/lapack/Makefile
config.status: creating src/nmath/Makefile
config.status: creating src/nmath/standalone/Makefile
config.status: creating src/scripts/Makefile
config.status: creating src/scripts/R.sh
config.status: creating src/scripts/Rcmd
config.status: creating src/scripts/javareconf
config.status: creating src/scripts/mkinstalldirs
config.status: creating src/scripts/pager
config.status: creating src/scripts/rtags
config.status: creating src/unix/Makefile
config.status: creating tests/Makefile
config.status: creating tests/Embedding/Makefile
config.status: creating tests/Examples/Makefile
config.status: creating tools/Makefile
config.status: creating src/include/config.h
config.status: src/include/config.h is unchanged
config.status: executing libtool commands
config.status: executing stamp-h commands
R is now configured for x86_64-pc-linux-gnu
Source directory: .
Installation directory: /usr/local
C compiler: gcc -g -O2
Fortran fixed-form compiler: gfortran -g -O2
Default C++ compiler: g++ -std=gnu++17 -g -O2
C++11 compiler: g++ -std=gnu++11 -g -O2
C++14 compiler: g++ -std=gnu++14 -g -O2
C++17 compiler: g++ -std=gnu++17 -g -O2
C++20 compiler: g++ -std=gnu++20 -g -O2
C++23 compiler: g++ -std=gnu++23 -g -O2
Fortran free-form compiler: gfortran -g -O2
Obj-C compiler:
Interfaces supported: X11, tcltk
External libraries: pcre2, readline, curl
Additional capabilities: PNG, JPEG, TIFF, NLS, cairo, ICU
Options enabled: shared BLAS, R profiling
Capabilities skipped:
Options not enabled: memory profiling
Recommended packages: yes
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