[R-sig-Debian] make check reg-tests-1b.R fails with Ubuntu R

[Andrew Piskorski]

Ah, with some different google searches, I found an older report of
this problem:

  http://r.789695.n4.nabble.com/R-2-12-0-beta-r53110-fails-make-check-on-Ubuntu-hardy-td2954249.html
  http://comments.gmane.org/gmane.comp.lang.r.devel/25646

Further below is the configure output from my from-source build.  It
says "External libraries:  [...]  BLAS(generic)", so apparently the
Ubuntu-provided BLAS is bad?  Really?!

I also don't know how to get that sort of configure information from
an already installed R.  Can you advise please?

I suspect R is linked against libraries from Ubuntu's libblas3gf
1.2-2build1 package (which is the Fortran 77 reference implementation,
modulo any Debian tweaks), but I'm not sure, and I don't know how to
check.  (Perhaps I need some magic ar, nm, or objdump incantation?)

I think my from-source builds on older versions of Ubuntu have used
the built-in BLAS provided by R, but something has switched it on me.
I suspect the main solution for me is to figure out how to either
switch back to the built-in BLAS, or to a faster optimized BLAS like
Atlas.

Any advice on how I should best straighten this would be appreciated...
Ideally, I'd like to fix both the stock Ubuntu R and my own
from-source installs.  However of the two, making the from-source
install correct is much more important to me.

On Wed, Sep 14, 2011 at 10:18:55AM -0400, Andrew Piskorski wrote:

> # R I just built from scratch, same failure as stock R:
> andy at n88:~$ /usr/local/pkg/R-2.12-branch-20110914/bin/R -q --vanilla
> > dtk.R.version()
> [1] "R 2.12.2 (Patched), 2011-03-18, svn.rev 57004, i686-pc-linux-gnu"

Here's the corresponding build configuration:
------------------------------------------------------------ 
R is now configured for i686-pc-linux-gnu  
 
  Source directory:          ..  
  Installation directory:    /usr/local/pkg/R-2.12-branch-20110914  
 
  C compiler:                gcc -std=gnu99  -g -O2  
  Fortran 77 compiler:       gfortran  -g -O2  
 
  C++ compiler:              g++  -g -O2  
  Fortran 90/95 compiler:    gfortran -g -O2  
  Obj-C compiler:               
 
  Interfaces supported:      X11, tcltk  
  External libraries:        readline, BLAS(generic), LAPACK(generic)  
  Additional capabilities:   PNG, JPEG, NLS  
  Options enabled:           shared R library, R profiling, Java  

-- 
Andrew Piskorski <atp at piskorski.com>
http://www.piskorski.com/