Cross-platform linking of a simple front-end

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Jon,

Dear all,

I have a simple front-end program which uses the APIs described in section
8 of "Writing R Extensions" to deviate from the standard R behaviour in
fairly minor ways. However, I'm having some difficulty getting it to link
reliably across different platforms.

R CMD LINK seemed like it would help, but I've had difficulty finding many
real-world examples online. I've tried

 R CMD LINK $(R CMD config CC) $(R CMD config --cppflags) $(R CMD config
--ldflags) -o ../bin/exec/tractor tractor.c

and this works on one of my test platforms (OS X.8.4, R 3.0.1), but not the
other (Ubuntu 12.04 LTS, R 2.14.1). In the latter case I get the error

 /usr/bin/ld: /tmp/ccmKf57E.o: undefined reference to symbol 'log10@
@GLIBC_2.0'
 /usr/bin/ld: note: 'log10@@GLIBC_2.0' is defined in DSO
/lib/i386-linux-gnu/libm.so.6 so try adding it to the linker command line
 /lib/i386-linux-gnu/libm.so.6: could not read symbols: Invalid operation
 collect2: ld returned 1 exit status

I can correct this by adding "-lm" manually to the command, but I'm not
sure how portable that will itself be.

My guess would be that you did not use --enable-R-shlib when compiling R on Ubuntu so you don't have a shared version of the R library to link against (which is needed to resolve the dependencies). Could that be the case?

Cheers,
Simon
Could anyone advise on the best way to make this work portably, please? For
this application I'm not concerned about Windows compatibility -
portability across Unix-alikes is sufficient. The source code is at <
https://github.com/jonclayden/tractor/blob/master/src/tractor.c>, if that
is useful.

All the best,
Jon

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Jon,

On Jul 4, 2013, at 10:52 AM, Jon Clayden wrote:

Dear all,

I have a simple front-end program which uses the APIs described in section
8 of "Writing R Extensions" to deviate from the standard R behaviour in
fairly minor ways. However, I'm having some difficulty getting it to link
reliably across different platforms.

R CMD LINK seemed like it would help, but I've had difficulty finding many
real-world examples online. I've tried

  R CMD LINK $(R CMD config CC) $(R CMD config --cppflags) $(R CMD config
--ldflags) -o ../bin/exec/tractor tractor.c

and this works on one of my test platforms (OS X.8.4, R 3.0.1), but not the
other (Ubuntu 12.04 LTS, R 2.14.1). In the latter case I get the error

  /usr/bin/ld: /tmp/ccmKf57E.o: undefined reference to symbol 'log10@
@GLIBC_2.0'
  /usr/bin/ld: note: 'log10@@GLIBC_2.0' is defined in DSO
/lib/i386-linux-gnu/libm.so.6 so try adding it to the linker command line
  /lib/i386-linux-gnu/libm.so.6: could not read symbols: Invalid operation
  collect2: ld returned 1 exit status

I can correct this by adding "-lm" manually to the command, but I'm not
sure how portable that will itself be.

My guess would be that you did not use --enable-R-shlib when compiling R on Ubuntu so you don't have a shared version of the R library to link against (which is needed to resolve the dependencies). Could that be the case?
I was able to reproduce this on Fedora: that is not the error if R was 
not built as a shared library.

I would simply copy how R does it (for R.bin in src/main).  libtool 
(used by R CMD LINK) is not coming up with the same flags.  On my system 
R is not using -lm:

gcc -std=gnu99 -Wl,--export-dynamic -fopenmp  -L/usr/local/lib64 -o 
R.bin Rmain.o  -L../../lib -lR -lRblas

Adding -lm is not portable (some OSes do not have a separate libm and 
some always add it when linking via $(CC)), but there is a LIBM macro in 
etc/Makeconf which tells you if configure found one.
Cheers,
Simon

Could anyone advise on the best way to make this work portably, please? For
this application I'm not concerned about Windows compatibility -
portability across Unix-alikes is sufficient. The source code is at <
https://github.com/jonclayden/tractor/blob/master/src/tractor.c>, if that
is useful.

All the best,
Jon

Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595
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