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ArtPoon / kamphir

Phylogenetic inference using a tree-shape kernel in an Approximate Bayesian Computation framework
BSD 3-Clause "New" or "Revised" License
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Seg fault in rcolgem, memory not mapped #19

Open ArtPoon opened 9 years ago

ArtPoon commented 9 years ago 
 *** caught segfault ***
address 0x7fd183cd9b88, cause 'memory not mapped'

Traceback:
 1: .Call("call_rkFixed", as.double(y), as.double(times), Func, Initfunc,     parms, Eventfunc, events, as.integer(Nglobal), rho, as.double(tcrit),     as.integer(vrb), as.double(hini), as.double(rpar), as.integer(ipar),     method, as.integer(nsteps), flist)
 2: rk(y, times, func, parms, method = "rk4", ...)
 3: ode(y = y0, c(h0, h1), func = "dQAL", parms = parameters, dllname = "rcolgem",     initfunc = "initfunc", method = integrationMethod)
 4: .solve.Q.A.L(h0, h1, A0, L)
 5: FUN(1:10[[2L]], ...)
 6: lapply(1:n.reps, run1)
 7: simulate.binary.dated.tree.fgy(tfgy[[1]], tfgy[[2]], tfgy[[3]],     tfgy[[4]], sampleTimes, sampleStates, integrationMethod = integrationMethod,     n.reps = nreps)
aborting ...
ArtPoon commented 9 years ago

This appears to be specific to the integration method (default rk4) used in simulate.binary.dated.tree.fgy, where ode() is called within function .solve.Q.A.L. If I set integrationMethod to adams then this problem does not occur.