VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon May 15 2006 - 12:13:49 CDT

Hi,
  It sounds like you're building on one of the new Linux distributions
which requires the use of -fPIC in the compiler flags. Edit the Make-arch
file and add -fPIC in the CCFLAGS and CXXFLAGS settings for the "LINUX:"
build target. Once you've done that, just do a "make clean" and build again
as before, and that should solve your problem. Let me know if you need
more help with this.

  John Stone
  vmd_at_ks.uiuc.edu

On Fri, May 12, 2006 at 02:19:47PM -0700, angel jiménez wrote:
> Dear friends:
>
> I have some problems to compile plugins from source.
>
> Here is what I did:
>
> First I installed tcl
> Second I set the environment variables:
> export TCLINC=/usr/include/
> export TCLLIB=/usr/lib/tcl8.4/
>
> Third In plugin directory:
> I typed: make LINUX
>
> Fourth
> I got this:
> Building Molecule File Reader plugins
> /usr/bin/ld: ../compile/lib_LINUX/molfile/biomoccaplugin.o: relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC
> ../compile/lib_LINUX/molfile/biomoccaplugin.o: could not read symbols: Bad value
> collect2: ld returned 1 exit status
> make[2]: *** [biomoccaplugin.so] Error 1
> /bin/sh: line 0: cd: apbsrun: No such file or directory
> /bin/sh: line 0: cd: atomedit: No such file or directory
> /bin/sh: line 0: cd: autoimd: No such file or directory
> /bin/sh: line 0: cd: autoionize: No such file or directory
> /bin/sh: line 0: cd: autopsf: No such file or directory
> /bin/sh: line 0: cd: biocore: No such file or directory
> etc......
>
> What am I doing wrong?
>
> Thanks a lot
>
>
>
>
>
>
>
>
>
>
> ---------------------------------
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-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078