Re: [R] Trouble compiling igraph. . .

From: Rainer Hurling <rhurlin_at_gwdg.de>
Date: Wed, 23 Jun 2010 14:37:07 +0200

On 23.06.2010 13:29 (UTC+1), jim smith wrote:
> Been and R-user for about 5 years now in an industrial setting, and
> always find the mailing list most helpful. I have run into problem
> compiling igraph on R. I have contacted the maintainer of igraph, and
> he has determined that it is not an igraph problem.
>
> System is FreeBSD 7.2, R-2.10.1 [also have a sandbox machine running
> FreeBSD 7.3, R-2.11]. Both machines fail the installation of igraph.
> Here is the error:

I am working with R-2.11.1 on FreeBSD 9.0-CURRENT (amd64). On several systems there had been no problems with installing igraph (0.5.3).

> Error in dyn.load(file, DLLpath = DLLpath, ...) :
> unable to load shared library
> '/usr/local/lib/R/library/igraph/libs/igraph.so': /usr/lib/libstdc+
> +.so.6: version GLIBCXX_3.4.11 required
> by /usr/local/lib/R/library/igraph/libs/igraph.so not found
> Error : .onLoad failed in 'loadNamespace' for 'igraph'
>
> I built the package, then ran the linker ldd to determine if libstdc+
> +.so.6 were in the correct place [and found by igraph]:
>
>
> libxml2.so.5 => /usr/local/lib/libxml2.so.5 (0x340e0000)
> libz.so.4 => /lib/libz.so.4 (0x33d89000)
> libiconv.so.3 => /usr/local/lib/libiconv.so.3 (0x3420a000)
> libR.so => /usr/local/lib/libR.so (0x34300000)
> libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0x3455c000)
> libm.so.5 => /lib/libm.so.5 (0x33d9b000)
> libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x33db0000)
> libc.so.7 => /lib/libc.so.7 (0x33c83000)
> libblas.so.2 => /usr/local/lib/libblas.so.2 (0x33dbb000)
> libgfortran.so.3 => /usr/local/lib/gcc44/libgfortran.so.3(0x34651000)
> libintl.so.8 => /usr/local/lib/libintl.so.8 (0x34709000)
> libreadline.so.7 => /lib/libreadline.so.7 (0x34712000)
> libpcre.so.0 => /usr/local/lib/libpcre.so.0 (0x34744000)
> liblzma.so.0 => /usr/local/lib/liblzma.so.0 (0x34778000)
> libbz2.so.3 => /usr/lib/libbz2.so.3 (0x347a1000)
> libicuuc.so.38 => /usr/local/lib/libicuuc.so.38 (0x347b2000)
> libicui18n.so.38 => /usr/local/lib/libicui18n.so.38 (0x348d0000)
> libncurses.so.7 => /lib/libncurses.so.7 (0x34a27000)
> libthr.so.3 => /lib/libthr.so.3 (0x34a66000)
> libicudata.so.38 => /usr/local/lib/libicudata.so.38 (0x34a7b000)

This is what I get from my igraph.so library:

#ldd /usr/local/lib/R/library/igraph/libs/igraph.so /usr/local/lib/R/library/igraph/libs/igraph.so:

         libxml2.so.5 => /usr/local/lib/libxml2.so.5 (0x41000000)
         libz.so.6 => /lib/libz.so.6 (0x4124b000)
         libiconv.so.3 => /usr/local/lib/libiconv.so.3 (0x41361000)
         libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0x4155b000)
         libm.so.5 => /lib/libm.so.5 (0x4176b000)
         libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x4188b000)
         libc.so.7 => /lib/libc.so.7 (0x40648000)

> So it appears to be there, but still I get this error. Any guidance?

The only idea I have is that there could be a problem with the compiler version you used to compile igraph. Perhaps R himself an igraph are build with different compilers?

> Thanks.

Hope this help a little bit,
Rainer



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