[R] Error when using foreach package for parralelization

[Julien Textoris]

Hi,

i tried to find the answer but didn't so my apologies if the question is 
obvious !

I'm trying to parallelize the following R code :

     pk2test = 
c(1:16,(12*16+1):(12*16+16),(16*16+1):(16*16+16),(20*16+1):(20*16+16))
     score.mat = matrix(nc=16*4,nr=16*4)
     for(i in 1:(16*4)) {

       for(j in i:(16*4)) {
           score.mat[i,j] = score.mat[j,i] =
             computeScore(pk[[pk2test[i]]],pk[[pk2test[j]]],10,5)$score
       }
     }

pk is a list of Object of type MassPeak from MALDIquant library. Each 
object is composed with a mass vector (@mass) an intensity vector 
(@intensity) and a metaData field (another list)

score.mat is a matrix with scores (reals)
pk2test is just a vector to know which objects in pk i want to deal with
computeScore is the function i wrote to compute the score, it calls 
another function called filterSpectra


I write the function like that, and i got the error below, and i can't 
figure out why ?

     pk2test = 
c(1:16,(12*16+1):(12*16+16),(16*16+1):(16*16+16),(21*16+1):(21*16+16))
     score.mat = matrix(nc=16*4,nr=16*4)
     for(i in 1:4) {
       score.mat[i,i:4] =
       foreach(filterSpectra=filterSpectra,
               computeScore=computeScore,
               pk=pk,pk2test=pk2test,i=i,j=c(i:4),
               .combine="c", .packages="MALDIquant" ) %dopar% {
           computeScore(pk[[pk2test[i]]],pk[[pk2test[j]]],10,5)$score
       }
     }

     Error: trying to get slot "mass" from an object of a basic class 
("integer") with no slots.

I think it is because when parallelizing, object are sent to child R 
session, but i don't understand how i have to write things to get it work.


If someone have a clue, it would be really appreciated and would let me 
save a lot of computing time !!

Thanks in advance,

Julien

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Julien Textoris
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