From watplatt at us.ibm.com  Mon Oct 16 21:47:01 2006
From: watplatt at us.ibm.com (watplatt at us.ibm.com)
Date: Mon, 16 Oct 2006 21:47:01 +0200 (CEST)
Subject: [Rd] PR#9295
Message-ID: <20061016194701.0CFDF561A2@slim.kubism.ku.dk>

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....

Dan

Saw:

IBM employee is unable to make AIX work: so why does he expect us to?

in response to:

From: watplatt at us.ibm.com
To: R-bugs at 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
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[Rd] PR#9295
watplatt at us.ibm.com