On Sat, 2005-09-17 at 17:19 -0500, Charles Geyer wrote:
> I can't compile R-alpha on AMD 64. Rather than include a 1400 line script
> I have put it on the web
>
> http://www.stat.umn.edu/~charlie/typescript.txt
>
> way down near the bottom it fails building lapack.so
>
> gcc -shared -L/usr/local/lib64 -o lapack.so Lapack.lo -llapack -lblas
> -lg2c -lm -lgcc_s
>
> /usr/lib64/gcc-lib/x86_64-suse-linux/3.3.5/../../../../x86_64-suse-linux/bin/ld:
>
> /usr/lib64/gcc-lib/x86_64-suse-linux/3.3.5/../../../../lib64/liblapack.a(dgecon.i):
> relocation R_X86_64_32 against `a local symbol' can not be used when making
> a shared object; recompile with -fPIC
> /usr/lib64/gcc-lib/x86_64-suse-linux/3.3.5/../../../../lib64/liblapack.a:
> could not read symbols: Bad value
>
> The 'recompile with -fPIC' is bullsh*t. The problem is that is is looking
> in /usr/lib64/liblapack.a rather than /usr/lib64/liblapack.so.3 both of which
> exist. Some searching for this error message on Google shows a lot of
> questions about this problem but no solution that I found other than
>
> rm /usr/lib64/liblapack.a
>
> which I don't consider a solution. It will link with the .so as the bottom
> of the script shows
>
> snowbank$ cd src/modules/lapack
> snowbank$ gcc -shared -o lapack.so Lapack.lo -llapack -lblas -lg2c -lm
> -lgcc_s
>
> /usr/lib64/gcc-lib/x86_64-suse-linux/3.3.5/../../../../x86_64-suse-linux/bin/ld:
>
> /usr/lib64/gcc-lib/x86_64-suse-linux/3.3.5/../../../../lib64/liblapack.a(dgecon.i):
> relocation R_X86_64_32 against `a local symbol' can not be used when making
> a shared object; recompile with -fPIC
> /usr/lib64/gcc-lib/x86_64-suse-linux/3.3.5/../../../../lib64/liblapack.a:
> could not read symbols: Bad value
> collect2: ld returned 1 exit status
> snowbank$ gcc -shared -o lapack.so Lapack.lo /usr/lib64/liblapack.so.3
> -lblas -l g2c -lm -lgcc_s
>
> No problems with the second link.
>
> So what do I do? liblapack.so is there. I've linked other (non-R) programs
> to it. So it SHOULD work with R.
>
> Either I can't read (possible) or the solution to this isn't in the gcc info
> pages.
>
> System (more info in typescript).
>
> AMD 64
> SuSE linux 9.3
> GCC 3.3.5
>
> I also observed the same problem with R-2.1.1 but didn't get around to
> debugging it until today.
>
> It occurred to me that /usr/local/lib/liblapack.so.3 which is 32 bit
> (because right now we are running only one R on both 32 and 64 bit and
> that's where the 32 bit R finds it's shared libraries), but I don't
> think that's the problem. Well maybe it is. How do I tell configure
> NOT to add /user/local ?
You would need to modify the LDFLAGS and CPPFLAGS environment variables,
as these default to -L/usr/local/lib and -I/usr/local/include
respectively. See Appendix B.3.3 of the R Installation and
Administration manual, which gives a warning about 64-bit systems.
You can also use the --with-readline configure flag to specify the exact
location of the readline library you wish to use.
I hope this helps.
Martyn
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