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R 3.6.0 for Debian buster

7 messages · Johannes Ranke, Dirk Eddelbuettel, Kurt Hornik

Original
Johannes Ranke
# 
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
Kurt Hornik
# 
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).  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

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Johannes Ranke
    

    

      
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Am Montag, 29. April 2019, 13:44:03 CEST schrieb Kurt Hornik:

            

      
      
      
    

        
No, I wasn't aware of this. Is there a bug report where this is discussed?

Johannes

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Kurt Hornik
    

    

      
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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 ...

Best
-k

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Johannes Ranke
    

    

      
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Am Montag, 29. April 2019, 15:03:54 CEST schrieb Kurt Hornik:

            

      
      
      
    

        
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

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Dirk Eddelbuettel
    

    

      
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On 29 April 2019 at 15:03, Kurt Hornik wrote:

        
| >>>>> 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 ...

            

      
      
      
    

        
A genuinely desirable feature (which can lead to improved performance from
'whole program' view) which however appears to have a side effect with older
Fortran code and its calling convention.

Note, however, that Debian unstable still has the 8.3.* branch. As such I
would find that it is a little early to ring alarm bells at full tilt. CCing
Martyn who use the R Foundation twitter handle for one such alarm.  Without
commensurate discussion on r-devel or r-package-devel this may not help much.

Dirk

| 
| 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 at r-project.org
| >> > https://stat.ethz.ch/mailman/listinfo/r-sig-debian
| 
| _______________________________________________
| R-SIG-Debian mailing list
| R-SIG-Debian at r-project.org
| https://stat.ethz.ch/mailman/listinfo/r-sig-debian

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Kurt Hornik
    

    

      
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Dirk: Martyn has a first tweet coming up shortly.

The change is actually not triggered by lto, but illustrated.  From what
we learned, calling Fortran from C without the additional character
length arguments for character arguments (as done in the R API) now
works differently as before, breaking at least about 25 CRAN packages,
half of which with segfaults.  And that compiler change is in the trunk
since several months but was ported to gcc-8-branch about a month ago,
and more or less immediately picked up in the gfortran-8 package in
testing/unstable ...

-k