[R-sig-Debian] R 3.6.0 for Debian buster

[Johannes Ranke]

Kurt,

Am Donnerstag, 9. Mai 2019, 16:35:24 CEST schrieb Kurt Hornik:
> >>>>> 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.

...

> 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.

Thanks, that sounds good. But I need some help as I do not know much about 
autoconf and Debian packaging: Is it enough to patch configure.ac (r76467) or 
do we need to update configure as well (r76468)?

> 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?

It seems to me this is of relevance for for Sébastien (Ccing), or more 
generally for debian-science.

Kind regards,

Johannes

> 
> 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 using r-project.org
> >> >> > https://stat.ethz.ch/mailman/listinfo/r-sig-debian
> >> 
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-- 
PD Dr. Johannes Ranke
Grenzach-Wyhlen