On Oct 27, 2014, at 16:55, Cyrus Harmon <[email protected]> wrote:
> In what I gather is a rite of passage for folks wishing to build/use coot,
> I'm running into some troubles trying to build coot from source. I think I've
> got the right prerequisites built and installed:
>
> mmdb2
> libccp4
> clipper-2.1
> ssm-1.4
> and of course the various prerequisites (python, gtk, etc...)
>
> When I try to build I coot, I get the following error message:
>
> make[1]: Entering directory
> '/home/sly/projects/structure/coot/coot-read-only/analysis'
> /bin/bash ../libtool --tag=CXX --mode=link g++ -o bfactan bfactan.o
> libcoot-analysis.la ../coot-utils/libcoot-coord-utils.la
> ../geometry/libcoot-geometry.la ../mini-mol/libcoot-mini-mol.la
> ../utils/libcoot-utils.la -L/usr/local/lib -lclipper-ccp4 -lclipper-cif
> -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs
> -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -L/usr/local/lib -lmmdb2
> libtool: link: g++ -o .libs/bfactan bfactan.o ./.libs/libcoot-analysis.so
> ../coot-utils/.libs/libcoot-coord-utils.so
> ../geometry/.libs/libcoot-geometry.so ../mini-mol/.libs/libcoot-mini-mol.so
> ../utils/.libs/libcoot-utils.so -L/usr/local/lib
> /usr/local/lib/libclipper-ccp4.so /usr/local/lib/libclipper-cif.so
> /usr/local/lib/libclipper-minimol.so /usr/local/lib/libclipper-mmdb.so
> /usr/local/lib/libclipper-cns.so /usr/local/lib/libclipper-phs.so
> /usr/local/lib/libclipper-contrib.so /usr/local/lib/libclipper-core.so
> /usr/local/lib/libccp4c.so /usr/local/lib/libmmdb2.so
> ../coot-utils/.libs/libcoot-coord-utils.so: undefined reference to
> `clipper::SFweight_spline<float>::operator()(clipper::HKL_data<clipper::datatypes::F_phi<float>
> >&, clipper::HKL_data<clipper::datatypes::F_phi<float> >&,
> clipper::HKL_data<clipper::datatypes::Phi_fom<float> >&,
> clipper::HKL_data<clipper::datatypes::F_sigF<float> > const&,
> clipper::HKL_data<clipper::datatypes::F_phi<float> > const&,
> clipper::HKL_data<clipper::datatypes::Flag> const&)'
> ../coot-utils/.libs/libcoot-coord-utils.so: undefined reference to
> `clipper::MMDBManager::cell() const'
> ../coot-utils/.libs/libcoot-coord-utils.so: undefined reference to
> `clipper::MMDBManager::spacegroup() const'
> ../coot-utils/.libs/libcoot-coord-utils.so: undefined reference to
> `clipper::SFweight_spline<float>::init(int, int, int)'
> collect2: error: ld returned 1 exit status
> Makefile:647: recipe for target 'bfactan' failed
> make[1]: *** [bfactan] Error 1
>
> I'm a bit at a loss trying to figure out the templated classes, etc... in
> sfweight.cpp so I thought I'd check to see if anyone else is having (or has
> run into) this problem. Also the clipper::MMDBxxx stuff make me wonder if
> this isn't the result of some stuff not yet being converted over to mmdb2.
> Pointers appreciated.
I think your guess is correct; I don’t know if this exactly matched the error
message I got when I accidentally compiled clipper against mmdb2, but it looks
like you may want to try mmdb1. I have 1.25.5 and 2.0.1 installed side-by-side.
// Johan
Research Specialist @ Gonen Lab
____________________________________________________
Janelia Research Campus * 19700 Helix Drive
Ashburn, VA 20147 * +1 (571) 209-4000 extension 3376
