Re: [R-sig-Debian] R 3.6.0 for Debian buster
On 9 May 2019 at 10:07, Dirk Eddelbuettel wrote:
| Kurt, there is one thing that has been bugging me too and I was wondering if
| I could lean on you as I have not had time work it out. It seems that one
| "should" be to set an environment variable to suppress additional
| "non-portable compiler flags used" warnings. We get those from Debian as
| distro-imposed flags I cannot ("should not") override; they are everywhere:
| Debian, backport, Ubuntu, Michael's PPA, hence Travis, ... and users are
| confused (see e.g. r-package-devel).
|
| Can you and I pretty-please work either a quick patch we fold in, or a set
| set via an environment variable in the Renviron.site we ship? I couldn't
| make the latter approach work yet.
|
| Example from most recent Travis build of mine:
| * checking compilation flags used ... NOTE
| Compilation used the following non-portable flag(s):
| ‘-Werror=format-security’ ‘-Wformat’
| * checking compiled code ... OK
|
| Source https://travis-ci.org/eddelbuettel/digest/builds/530216741
|
| Happy to take off-list.
I would appear that I had forgotten that I had half-fixed that. My
~/.R/check.Renviron contains this at the end
[... stuff omitted ...]
#
# edd Apr 2019
_R_CHECK_COMPILATION_FLAGS_=TRUE
_R_CHECK_COMPILATION_FLAGS_KNOWN_="-Wno-class-memaccess -Wno-ignored-attributes
-Wno-misleading-indentation -Wno-unused"
so presumably carrying that line over would help. Sebastian Meyer also kind
sent me pretty mich the same line off-list which he had added to his
~/.Renviron.
Dirk
--
http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
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Re: [R-sig-Debian] R 3.6.0 for Debian buster
On 9 May 2019 at 16:35, Kurt Hornik wrote:
| > Johannes Ranke writes:
|
| Johannes,
|
| It seems that one can avoid the gfortran problems with Fortran
| BLAS/LAPACK implementations by compiling with
| -fno-optimize-sibling-calls.
|
| Tomas recently wrote to R Core that
|
| *
| - gfortran is leaning to (but no official announcement decision has
| already been reached) making -fno-optimize-sibling-calls the default as
| not to break BLAS/LAPACK, at least temporarily to give BLAS/LAPACK
| authors some time to fix
|
| - gfortran developers started discussing the issue with reference lapack
| maintainers on github, suggesting that the reference should use wrappers
| using portable C bindings using BIND(C) (which I've been suggesting to
| the gfortran developers as I saw it in "Numerical Computing with Modern
| Fortran" but of course they would have known too)
| *
|
| See
|
| https://github.com/Reference-LAPACK/lapack/issues/339
| https://gcc.gnu.org/bugzilla/show_bug.cgi?id=90329
|
| for more information.
|
| Yesterday I changed R-devel and R-patched to use
| -fno-optimize-sibling-calls for gfortran >= 7: it would be great if you
| could pull this change into the R 3.6.0 backports for buster.
|
| In principle I think all Fortran BLAS/LAPACK implementations (refblas
| and ATLAS) packaged for buster should be recompiled with
| -fno-optimize-sibling-calls (they may be fine in case they were compiled
| with older version of gfortran-8, but then the next rebuild will cause
| trouble): Dirk, any chance you could get the package maintainers to make
| these changes?
If I make them in Debian package it usually just flows to Johannes (for
Debian backports) and Michael (for Ubuntu) as those two gentlemen are very
reliable too.
Kurt, there is one thing that has been bugging me too and I was wondering if
I could lean on you as I have not had time work it out. It seems that one
"should" be to set an environment variable to suppress additional
"non-portable compiler flags used" warnings. We get those from Debian as
distro-imposed flags I cannot ("should not") override; they are everywhere:
Debian, backport, Ubuntu, Michael's PPA, hence Travis, ... and users are
confused (see e.g. r-package-devel).
Can you and I pretty-please work either a quick patch we fold in, or a set
set via an environment variable in the Renviron.site we ship? I couldn't
make the latter approach work yet.
Example from most recent Travis build of mine:
* checking compilation flags used ... NOTE
Compilation used the following non-portable flag(s):
‘-Werror=format-security’ ‘-Wformat’
* checking compiled code ... OK
Source https://travis-ci.org/eddelbuettel/digest/builds/530216741
Happy to take off-list.
Dirk
| Best
| -k
|
|
|
|
| > Am Montag, 29. April 2019, 15:03:54 CEST schrieb Kurt Hornik:
| >> > Johannes Ranke writes:
| >> > Am Montag, 29. April 2019, 13:44:03 CEST schrieb Kurt Hornik:
| >> >> > Johannes Ranke writes:
| >> >> Thanks. You may have seen that with current gfortran in
| >> >> testing/unstable, there are problems with the R BLAS/LAPACK API entries
| >> >> using a Fortran interface (and hence in particular when using the BLAS
| >> >> and LAPACK sources that ship with R).
| >> >
| >> > No, I wasn't aware of this. Is there a bug report where this is
| >> > discussed?
| >>
| >> Not really, as the issue seems to complicated to condense into a bug
| >> report. From discussions with Thomas Koenig from the GCC team, it seems
| >> that f2c, g77 and now gfortran have always added additional character
| >> length arguments for each character argument, where the R
| >> F77_NAME/F77_CALL mechanism has always called with the arguments of the
| >> Fortran subroutine but without the additional length arguments. A
| >> change in gcc trunk also ported to gcc-8-branch apparently changed what
| >> happened in such case, to the effect that we're now seeing about 25
| >> CRAN packages fail their run time checks with segfaults or run time
| >> errors ...
| >>
| >> But things are actually hard to pin down for us, and no obvious "fix"
| >> is in sight. It would be great if at least for the gfortran-8 that
| >> Debian will release we would get the old behavior back ...
|
| > I think the likelihood of this would be greater if there was a bug against
the
| > version of gfortran in unstable/testing... Can you give a small
reproducible
| > example?
|
| > Johannes
|
| >>
| >> Best
| >> -k
| >>
| >> > Johannes
| >> >
| >> >> It seems I can avoid these using
| >> >> OpenBLAS (but then this really only works find for me provided I setenv
| >> >> OPENBLAS_NUM_THREADS=1).
| >> >>
| >> >> -k
| >> >>
| >> >> > Dear all,
| >> >> > Now that the upcoming Debian release "buster" is frozen, I have
started
| >> >> > supplying backports for it. Pending mirror
Re: [R-sig-Debian] R 3.6.0 for Debian buster
> Johannes Ranke writes: Johannes, It seems that one can avoid the gfortran problems with Fortran BLAS/LAPACK implementations by compiling with -fno-optimize-sibling-calls. Tomas recently wrote to R Core that * - gfortran is leaning to (but no official announcement decision has already been reached) making -fno-optimize-sibling-calls the default as not to break BLAS/LAPACK, at least temporarily to give BLAS/LAPACK authors some time to fix - gfortran developers started discussing the issue with reference lapack maintainers on github, suggesting that the reference should use wrappers using portable C bindings using BIND(C) (which I've been suggesting to the gfortran developers as I saw it in "Numerical Computing with Modern Fortran" but of course they would have known too) * See https://github.com/Reference-LAPACK/lapack/issues/339 https://gcc.gnu.org/bugzilla/show_bug.cgi?id=90329 for more information. Yesterday I changed R-devel and R-patched to use -fno-optimize-sibling-calls for gfortran >= 7: it would be great if you could pull this change into the R 3.6.0 backports for buster. In principle I think all Fortran BLAS/LAPACK implementations (refblas and ATLAS) packaged for buster should be recompiled with -fno-optimize-sibling-calls (they may be fine in case they were compiled with older version of gfortran-8, but then the next rebuild will cause trouble): Dirk, any chance you could get the package maintainers to make these changes? Best -k > Am Montag, 29. April 2019, 15:03:54 CEST schrieb Kurt Hornik: >> > Johannes Ranke writes: >> > Am Montag, 29. April 2019, 13:44:03 CEST schrieb Kurt Hornik: >> >> > Johannes Ranke writes: >> >> Thanks. You may have seen that with current gfortran in >> >> testing/unstable, there are problems with the R BLAS/LAPACK API entries >> >> using a Fortran interface (and hence in particular when using the BLAS >> >> and LAPACK sources that ship with R). >> > >> > No, I wasn't aware of this. Is there a bug report where this is >> > discussed? >> >> Not really, as the issue seems to complicated to condense into a bug >> report. From discussions with Thomas Koenig from the GCC team, it seems >> that f2c, g77 and now gfortran have always added additional character >> length arguments for each character argument, where the R >> F77_NAME/F77_CALL mechanism has always called with the arguments of the >> Fortran subroutine but without the additional length arguments. A >> change in gcc trunk also ported to gcc-8-branch apparently changed what >> happened in such case, to the effect that we're now seeing about 25 >> CRAN packages fail their run time checks with segfaults or run time >> errors ... >> >> But things are actually hard to pin down for us, and no obvious "fix" >> is in sight. It would be great if at least for the gfortran-8 that >> Debian will release we would get the old behavior back ... > I think the likelihood of this would be greater if there was a bug against > the > version of gfortran in unstable/testing... Can you give a small reproducible > example? > Johannes >> >> Best >> -k >> >> > Johannes >> > >> >> It seems I can avoid these using >> >> OpenBLAS (but then this really only works find for me provided I setenv >> >> OPENBLAS_NUM_THREADS=1). >> >> >> >> -k >> >> >> >> > Dear all, >> >> > Now that the upcoming Debian release "buster" is frozen, I have started >> >> > supplying backports for it. Pending mirror synchronisations, R 3.6.0 is >> >> > now >> >> > available for Debian buster on i386 and amd64 architectures. Please >> >> > refer >> >> > to> >> >> > >> >> > https://cran.r-project.org/bin/linux/debian/ >> >> > >> >> > for details. At the moment I am not providing binaries for the arm >> >> > architecture for buster, as the SD card in my raspberry 3 has died and >> >> > I >> >> > do >> >> > not use these binaries any more anyways. Let me know if this is a >> >> > problem. >> >> > >> >> > Kind regards, >> >> > >> >> > Johannes >> >> > >> >> > ___ >> >> > R-SIG-Debian mailing list >> >> > R-SIG-Debian@r-project.org >> >> > https://stat.ethz.ch/mailman/listinfo/r-sig-debian >> >> ___ >> R-SIG-Debian mailing list >> R-SIG-Debian@r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-debian > -- > PD Dr. Johannes Ranke > Grenzach-Wyhlen ___ R-SIG-Debian mailing list R-SIG-Debian@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-debian
