Call FORTRAN subroutine with allocatables in R? - r

Question

This is a follow-up question to my previous Fortran question.
I have a working Fortran program that has a subroutine that filters an array. This is the program:
program test
integer, parameter :: n = 3
integer, parameter :: m = 4
double precision, dimension(n,m) :: A
double precision, dimension(:,:), allocatable :: B
A(1,:) = [11, 22, 43, 55]
A(2,:) = [15, 56, 65, 63]
A(3,:) = [54, 56, 32, 78]
print*, 'A :'
print*, int(A)
CALL extractB(A, B)
print*, 'B'
print*, int(B)
contains
subroutine extractB(A, B)
implicit none
double precision, dimension(:,:), intent(in) :: A
double precision, dimension(:,:), allocatable :: B
integer :: nrowB, i, pos
nrowB = count( A(:,2)==56)
allocate( B(nrowB, size(A,2)-1 ) )
pos = 1
do i = 1, size(A,1)
if(A(i,2)==56)then
B(pos,1) = A(i,1)
B(pos,2:) = A(i,3:)
pos = pos+1
end if
end do
end subroutine extractB
end program
The program compiles, runs, and it does what it has to do very well.
I want to call the extractB subroutine with R. I have asked similar questions and found was able to make them work, but this one is somehow different and not working.
My fortran subrutine is in the mytest.f90 file and has this code:
subroutine extractB(A, B)
implicit none
double precision, dimension(:,:), intent(in) :: A
double precision, dimension(:,:), allocatable :: B
integer :: nrowB, i, pos
nrowB = count( A(:,2)==56)
allocate( B(nrowB, size(A,2)-1 ) )
pos = 1
do i = 1, size(A,1)
if(A(i,2)==56)then
B(pos,1) = A(i,1)
B(pos,2:) = A(i,3:)
pos = pos+1
end if
end do
end subroutine extractB
I compile it in R and load the library with these commands:
system("R CMD SHLIB ./Fortran/mytest.f90")
dyn.load("./Fortran/mytest.so")
Then, in R, i create and pass a data frame to the subroutine
A = data.frame(c(11,15,54), c(22,56,56), c(43,65,32), c(55,63,78))
X<-.Fortran("extractB", A = unlist(A), B = numeric(6))
After that R crashes
*** caught segfault ***
address (nil), cause 'unknown'
Traceback:
1: .Fortran("extractB", A = unlist(A), B = numeric(6))
Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection:
If I change the subroutine by removing setting the dimensions by hand:
subroutine extract(A, B)
implicit none
double precision, dimension(3,4), intent(in) :: A
double precision, dimension(2,3) :: B
integer :: i, pos
pos = 1
do i = 1, size(A,1)
if(A(i,2)==56)then
B(pos,1) = A(i,1)
B(pos,2:) = A(i,3:)
pos = pos+1
end if
end do
end subroutine extract
recompile the library, and reload it. I can run
X<-.Fortran("extract", A = unlist(A), B = numeric(6))
dim(X$A) <- dim(A)
dim(X$B) <- c(2,3)
and get what I want
> X
$A
[,1] [,2] [,3] [,4]
[1,] 11 22 43 55
[2,] 15 56 65 63
[3,] 54 56 32 78
$B
[,1] [,2] [,3]
[1,] 15 65 63
[2,] 54 32 78
Any way of fixing this?
Thanks a lot for the help!

Answer 1

Though, as Vladimir F pointed out, this will not work with allocatables like this, you can allocate memory, that can be used by another language in Fortran. But you should use the pointer attribute in that case. However, you will not be able to make use of assumed shape arrays either. Instead of inferring the size of A, you should pass it in explicitly.
If you are willing to change the interface for this, you can get your functionality with something along these lines, (see also M. S. B.s answer to a related question):
subroutine extractB(A_ptr, lenX, lenY, B_ptr, nrowB) bind(c,name=extractB)
use iso_c_binding
implicit none
type(c_ptr), value :: A_ptr
integer(kind=c_int), value :: lenX, lenY
type(c_ptr) :: B_ptr
integer(kind=c_int) :: nrowB
real(kind=c_double), pointer :: A(:,:)
real(kind=c_double), pointer :: B(:,:)
integer :: i, pos
c_f_pointer(A_ptr, A, [lenX, lenY])
nrowB = count( A(:,2)==56)
allocate( B(nrowB, size(A,2)-1 ) )
!...
B_ptr = c_loc(B)
end subroutine extractB