[BioC] Writing R Extensions : problems

Richard Finney rfinney5 at yahoo.com
Thu Jun 10 20:51:26 CEST 2004

I am trying to implement an extension to R
which I hope to make into a bioconductor package.
The program will process Qstar proteomics data.
I wish to implement a function called "binandnorm".
However, I'm getting an unresolved symbol.  The
symbol is  "TYPEOF__FP7SEXPREC".  This problem 
appears on 1.8.1and 1.9.0 version of R.  I have
installed bioconductor.

    I have compiled the program using the 
    SHLIB R command feature ... which apparently 
    does this ..

g++ -I/usr/local/lib/R/include  -I/usr/local/include  
-fPIC  -g -O2 -c binandnorm.cpp -o binandnorm.o
g++ -G -L/usr/local/lib -o binandnorm.so binandnorm.o 
 -L/usr/local/lib/R/bin -lR

    I do this to dump some symbols for later 
    reference ...

elfdump *.so > junk

    I am running on a Sun box using R.1.8.1 ...

uname -a
SunOS xxxxxxxxxx.xxx.nih.gov 5.8 Generic_108528-16
sun4u sparc SUNW,Sun-Fire

    I run the R command

bash-2.03$ R

R : Copyright 2003, The R Foundation for Statistical
Version 1.8.1  (2003-11-21), ISBN 3-900051-00-3

R is free software and comes with ABSOLUTELY NO
 [blah .. blah .. blah ...] 
Type 'q()' to quit R.

> version
platform sparc-sun-solaris2.8
arch     sparc
os       solaris2.8
system   sparc, solaris2.8
major    1
minor    8.1
year     2003
month    11
day      21
language R
> dyn.load("binandnorm.so")
Error in dyn.load(x, as.logical(local),
as.logical(now)) :
        unable to load shared library
  ld.so.1: /usr/local/lib/R/bin/R.bin: fatal:
relocation error: file
/h1/finneyr/BINANDQ/src/binandnorm.so: symbol
TYPEOF__FP7SEXPREC: referenced symbol not found
> q()
Save workspace image? [y/n/c]: n

    Rrrgghh !!!!  Well, let's see if we can find

bash-2.03$ grep -i TYPEOF__FP7SEXPREC *

    nothing.  rrrgghhhh.

    try fgrep ...


     oh.  okay.  it is there.  the symbol exists
in the object file.  why can't it get resolved
when loaded into R ???

Anyone know what's up with this? 

I can trim down the R interface code in the C file to
something like this ...

SEXP binandnorm(SEXP SEXPalgorithm, SEXP SEXPqsize1,
    SEXP SEXPqsize2, SEXP SEXPoutputoption,
    SEXP SEXPoutputfilename, SEXP SEXPfilenames)
    SEXP ans;
    ans = PROTECT(allocMatrix(REALSXP, 1, 1));
    return NULL;

and when I do the dyn.load() from R I get this ...
  ... (blah blah ..) ... ld.so.1:
/h1/finneyr/R-1.9.0/bin/R.bin: fatal: relocation
error: file
/h1/finneyr/R-1.9.0/BINANDQ/src/binandnorm.so: symbol
Rf_allocMatrix__FUiii: referenced symbol not found

    That symbol Rf_allocMatrix__FUiii really is 
there ...

bash-2.03$ fgrep -l Rf_allocMatrix__FUiii *

    I'm not sure what's up with the symbol
extension "FUiii".  What's generating that?

    If anybody has any knowledge or wild guesses as
to what's going on here, I'd appreciate it.


-Richard Finney

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