I'm glad I didn't see those comments -- ;-)

Prof. Ripley also pointed out they weren't supposed to be macros.

The -bexpall (actuall -Wl,-bexpall) produced an effect: now it complains 
about finding fortran libraries.  gfortran was compiled with static libs 
on this system.  It is complaining as well about lapack-like names dger_, 
dgemv_.  This failure is happening around grDevices:

make[4]: Leaving directory 
`/geno4/watplatt/R/R-2.4.0/src/library/grDevices/src'
Error in solve.default(rgb) : lapack routines cannot be loaded
In addition: Warning message:
unable to load shared library 
'/geno4/watplatt/R/R-2.4.0/modules//lapack.so':
  rtld: 0712-001 Symbol _gfortran_pow_r8_i4 was referenced
      from module /geno4/watplatt/R/R-2.4.0/lib/libRlapack.so(), but a 
runtime definition
      of the symbol was not found.
rtld: 0712-001 Symbol _gfortran_compare_string was referenced
      from module /geno4/watplatt/R/R-2.4.0/lib/libRlapack.so(), but a 
runtime definition
      of the symbol was not found.
rtld: 0712-001 Symbol _gfortran_copy_string was referenced
      from module /geno4/watplatt/R/R-2.4.0/lib/libRlapack.so(), but a 
runtime definition
      of the symbol was not found.
rtld: 0712-001 Symbol dger_ was referenced
      from module /geno4/watplatt/R/R-2.4.0/lib/libRlapack.so(), but a 
runtime definition
      of the symbol was not found.
rtld: 0712-001 Symbol dgemv_ was referenced
      from module /geno4/watplatt/R/R-2.4.0/lib/libRlapack.so(), but a 
runtime definition
      of the symbol was not found.
rtld: 0712-001 Symbol _gfortr 
Error: unable to load R code in package 'grDevices'
Execution halted

The directory path to lapack.so appears to be correct, not in a path 
connected to other builds or versions, etc.  The file lapack.so is sitting 
in the directory as spec'd in the complaint.

Daniel E. Platt
Bioinformatics and Pattern Discovery
IBM T. J. Watson Research Center
Yorktown Hgts, NY 10598
(914)945-1388



Peter Dalgaard <p.dalgaard@biostat.ku.dk> 
Sent by: pd@pubhealth.ku.dk
10/16/2006 04:29 PM

To
Daniel Platt/Watson/IBM@IBMUS
cc
r-devel@stat.math.ethz.ch, R-bugs@biostat.ku.dk
Subject
Re: [Rd] PR#9295






watplatt@us.ibm.com writes:

> I asked a question that might help me track down what changed between 
> 2.3.1 that did build and the 2.4.0 version that will not build.  Some of 

> the undefined names the linker was complaining about looked like #define 

> symbols that were not picked up by configure.  The first thing I was 
> hoping for was to find out if this problem looked familiar?  Whether or 
> not, I'm willing to try to work on it, but hope I can get reasonable 
> answers to honest questions....

Well, you should have seen the snide remarks that I decided to keep to
myself.... (Along the lines of "please tell us the fix in time for the
_next_ release")

Anyways, AFAIK those entry points are not supposed to be macros. They
are also undefined symbols in tools.so on Fedora, so your issue would
seem to be with the linker. The culprit is likely changes to the
symbol registration mechanism, or an unforeseen complication of this:

    o   configure now defaults to 'run-time linking' on AIX
        (and AIX < 4.2 is no longer allowed), using -bexpall rather
        than export/import files.  If this works, it allows R to be
        built in the same way as other Unix-alikes, including with R
        as a shared library and with a shared BLAS.

Also, of course, check that you are doing a clean build and that the
previous build is not somehow interfering.
 
> Dan
> 
> Saw:
> 
> IBM employee is unable to make AIX work: so why does he expect us to?
> 
> in response to:
> 
> From: watplatt@us.ibm.com
> To: R-bugs@biostat.ku.dk
> Subject: Unable to build
> Date: Fri, 13 Oct 2006 21:42:37 +0200 (CEST)
> 
> Full_Name: Daniel E. Platt
> Version: 2.4.0
> OS: AIX 5.3
> Submission from: (NULL) (129.34.20.23)
> 
> 
> Did a new build of gcc c,c++,gfortran v4.1.1, (re)built R 2.3.1 using
> config.site as spec'd in R-admin.pdf in sec C.9 as described by Jagat 
> Sheth,
> with addition of FC=gfortran (configure tried using f95, which is 
present 
> on the
> system, but won't bind with gcc's obj files).
> 
> 
> Applying the same to 4.1.1 produces the following:
> 
> make[4]: Leaving directory 
> `/geno4/watplatt/R/R-2.4.0/src/library/tools/src'
> Error in dyn.load(x, as.logical(local), as.logical(now)) : 
>         unable to load shared library
> '/geno4/watplatt/R/R-2.4.0/library/tools/libs/tools.so':
>   rtld: 0712-001 Symbol TYPEOF was referenced
>       from module 
/geno4/watplatt/R/R-2.4.0/library/tools/libs/tools.so(), 
> but a
> runtime definition
>       of the symbol was not found.
> rtld: 0712-001 Symbol Rf_error was referenced
>       from module 
/geno4/watplatt/R/R-2.4.0/library/tools/libs/tools.so(), 
> but a
> runtime definition
>       of the symbol was not found.
> rtld: 0712-001 Symbol Rf_asLogical was referenced
>       from module 
/geno4/watplatt/R/R-2.4.0/library/tools/libs/tools.so(), 
> but a
> runtime definition
>       of the symbol was not found.
> rtld: 0712-001 Symbol LENGTH was referenced
>       from module 
/geno4/watplatt/R/R-2.4.0/library/tools/libs/tools.so(), 
> but a
> runtime definition
>       of the symbol was not found.
> rtld: 0712-001 Symbol STRING_ELT was referenced
>       from module 
/geno4/watplatt/R/R-2.4.0/library/tools/libs/tools.so(), 
> bu
> Execution halted
> make[3]: *** [all] Error 1
> make[3]: Leaving directory `/geno4/watplatt/R/R-2.4.0/src/library/tools'
> make[2]: *** [R] Error 1
> make[2]: Leaving directory `/geno4/watplatt/R/R-2.4.0/src/library'
> make[1]: *** [R] Error 1
> make[1]: Leaving directory `/geno4/watplatt/R/R-2.4.0/src'
> make: *** [R] Error 1
> 
> Are there undefined #define's leaking in as code?
> 
> Dan
> 
> 
> 
> 
> Daniel E. Platt
> Bioinformatics and Pattern Discovery
> IBM T. J. Watson Research Center
> Yorktown Hgts, NY 10598
> (914)945-1388
>                [[alternative HTML version deleted]]
> 
> ______________________________________________
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
> 

-- 
   O__  ---- Peter Dalgaard             Øster Farimagsgade 5, Entr.B
  c/ /'_ --- Dept. of Biostatistics     PO Box 2099, 1014 Cph. K
 (*) \(*) -- University of Copenhagen   Denmark          Ph:  (+45) 
35327918
~~~~~~~~~~ - (p.dalgaard@biostat.ku.dk)                  FAX: (+45) 
35327907


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