You are correct: there is no reason to assume that the F90 compiler
can link C++ nor that the C++ compiler can link F90, and in general
they cannot. Quite a few systems have a different vendor's F9x
compiler (including say g95 vs gcc3 and SunPro F9x vs gcc4).
Even in a pure gcc4 scenario, each of F9x and C++ needs additional
libaries and R does not know what they are (it only does for F77).
So if linking by g++ works for you, it is fortuitous and not portable.
I suspect adding -lstdc++ will work for you, which you can do via
PKG_LIBS in a Makevars file.
Bottom line: you are asking to do something known not to be portable.
You can use a Makefile to have complete freedom, but please don't
distribute such a package without a configure script to check out all
the assumptions.
On Fri, 9 Jan 2009, Steve Guerrero wrote:
Sorry I was a little stingy with details.
I'm building a very simple package on linux with R 2.7.1
Still no details of compilers etc.
no configure script or homemade makefiles.
my src directory has two files:
src/foo.cpp
src/bar.f90
I run "R CMD install myproject " which runs fine, no errors, and produces a
shared library
i.e.:
gfortran -fdefault-real-8 -ffixed-form -fpic -g -O2 -c GLMnet.f90 -o bar.f90
g++ (all the right flags) -fpic -g -O2 -c foo.cpp -o foo.o
and the link step:
gfortran -shared -L/usr/local/lib64 -o myproject.so baro foo.o
-L/apps/R/R-2.7.1/x86_64-linux-2.6/lib64/R/lib -lR
The build goes fine, the problem is when I load the library I get this error:
library(myproject)
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared library myproject.so
undefined symbol: __gxx_personality_v0
Error: package/namespace load failed for 'myproject'
If I manually run the link step with g++ instead of gfortran, the library
loads fine, everything works.
I need to tell the R build process to not link with gfortran but to link with
g++ in my mixed c++ and fortran scenario. A little digging into the R SHLIB
build script suggests that I probably can't override it without cooking up my
Makefiles
Here's an excerpt from the R SHLIB script:
makeargs="SHLIB=\"${shlib}\""
if ${with_f9x}; then
makeargs="SHLIB_LDFLAGS='\$(SHLIB_FCLDFLAGS)' ${makeargs}"
makeargs="SHLIB_LD='\$(SHLIB_FCLD)' ${makeargs}"
else
if ${with_cxx}; then
makeargs="SHLIB_LDFLAGS='\$(SHLIB_CXXLDFLAGS)' ${makeargs}"
makeargs="SHLIB_LD='\$(SHLIB_CXXLD)' ${makeargs}"
fi
if ${with_f77}; then
if ${with_objc}; then
shlib_libadd="\$(OBJC_LIBS) ${shlib_libadd}"
fi
if test -z "${shlib_libadd}"; then
makeargs="${makeargs} SHLIB_LIBADD='\$(FLIBS)'"
else
makeargs="${makeargs} SHLIB_LIBADD='\$(FLIBS) ${shlib_libadd}'"
fi
else
if ${with_objc}; then
makeargs="${makeargs} SHLIB_LIBADD='\$(OBJC_LIBS)'"
fi
fi
fi
This logic seems to suggest that if there are fortran95 sources, the LD
command will be SHLIB_FCLD...with no apparent way to override it.
Am I mistaken?
Thanks,
-sg
Duncan Murdoch wrote:
On 09/01/2009 4:04 PM, Steve Guerrero wrote:
I'm trying to build a package which has both gfortran and c++ code.
In my installation of R, the R CMD INSTALL process compiles each c++ and
gfortran code with the correct compiler, but performs the link step with
"gfortran" and this creates undefined symbols at load time.
You should offer more details: what platform are you working on? What
version of R? Do you have a simple example that people could try, and see
the errors?
Duncan Murdoch
How does one override/force the use of a different command in the link
step? Is there an appropriate entry in Makevars that will do the trick?
Thanks,
-sg
______________________________________________
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
______________________________________________
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
--
Brian D. Ripley, rip...@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
______________________________________________
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
