Confusing error messages when with linking with LTO?

[Benjamin Redelings I <benjamin dot redelings at nescent dot org>]

Hi,

    I just tried compiling with LTO for the first time.  I can't figure 
out what to try based on the error message below.  Is there a HTML page 
I should be looking at?

It seems that this did not work:

g++-4.6  -isystem ../../../master/boost/include -ffast-math -DNDEBUG 
-DNDEBUG_DP -funroll-loops -fweb -flto -fuse-linker-plugin 
-march=native  -pipe -O3  -isystem /usr/lib/openmpi/include -isystem 
/usr/lib/openmpi/include/openmpi -pthread -pedantic -pthread 
-I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include 
-I/usr/include/pixman-1 -I/usr/include/freetype2 
-I/usr/include/libpng12   -Wall -Wextra -Wno-sign-compare 
-Woverloaded-virtual -Wstrict-aliasing   -o alignment-gild 
alignment-gild.o alignment.o alphabet.o sequence.o util.o rng.o tree.o 
sequencetree.o optimize.o findroot.o setup.o imodel.o probability.o 
sequence-format.o model.o distance-methods.o alignment-random.o 
alignment-util.o randomtree.o tree-util.o inverse.o io.o  
../boost/lib/filesystem/libboost_filesystem.a 
../boost/lib/program_options/libboost_program_options.a -lgsl -lgslcblas 
-lm
/usr/bin/ld.gold: error: /tmp/cc4IJUrh.ltrans12.ltrans.o: multiple 
definition of '_ZTV18RootedSequenceTree.local.4048'
/usr/bin/ld.gold: /tmp/cc4IJUrh.ltrans7.ltrans.o: previous definition here
/usr/bin/ld.gold: error: /tmp/cc4IJUrh.ltrans12.ltrans.o: multiple 
definition of '_ZTT18RootedSequenceTree.local.4049'
/usr/bin/ld.gold: /tmp/cc4IJUrh.ltrans7.ltrans.o: previous definition here
collect2: ld returned 1 exit status

So, it looks like the virtual table for class RootedSequenceTree is 
defined in multiple places.  But the file name 
cc4IJUrh.ltrans12.ltrans.o doesn't clearly correspond to any input file 
name.  Is there any way for me to find out which *.o files have 
definitions for this symbol, and why they are problematic only with LTO?

-BenRI

P.S. Apparently this did work:

g++-4.6  -isystem ../../../master/boost/include -ffast-math -DNDEBUG 
-DNDEBUG_DP -funroll-loops -fweb -flto -fuse-linker-plugin 
-march=native  -pipe -O3  -isystem /usr/lib/openmpi/include -isystem 
/usr/lib/openmpi/include/openmpi -pthread -pedantic -pthread 
-I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include 
-I/usr/include/pixman-1 -I/usr/include/freetype2 
-I/usr/include/libpng12   -Wall -Wextra -Wno-sign-compare 
-Woverloaded-virtual -Wstrict-aliasing   -o bali-phy sequence.o tree.o 
alignment.o substitution.o moves.o rng.o exponential.o eigenvalue.o 
parameters.o likelihood.o mcmc.o choose.o sequencetree.o 
sample-branch-lengths.o util.o randomtree.o alphabet.o smodel.o 
bali-phy.o hmm.o dp-engine.o dp-array.o dp-matrix.o 3way.o 2way.o 
sample-alignment.o sample-tri.o sample-node.o imodel.o 5way.o 
sample-topology-NNI.o setup.o rates.o matcache.o sample-two-nodes.o 
sequence-format.o util-random.o alignment-random.o setup-smodel.o 
sample-topology-SPR.o alignment-sums.o alignment-util.o probability.o 
model.o alignment-constraint.o substitution-cache.o substitution-star.o 
monitor.o substitution-index.o tree-util.o myexception.o pow2.o 
partition.o proposals.o n_indels.o distribution.o parsimony.o version.o 
slice-sampling.o timer_stack.o setup-mcmc.o io.o logger.o AIS.o  
../boost/lib/mpi/libboost_mpi.a 
../boost/lib/serialization/libboost_serialization.a -pthread 
-L/usr/lib/openmpi/lib -lmpi_cxx -lmpi -lopen-rte -lopen-pal -ldl 
-Wl,--export-dynamic -lnsl -lutil -lm -ldl  
../boost/lib/filesystem/libboost_filesystem.a 
../boost/lib/program_options/libboost_program_options.a -lgsl -lgslcblas -lm

If I don't use LTO (that is, if I remove "-flto -fuse-linker-plugin") 
then everything works.