I have searched and have seen similar errors but nothing specific as to how to fix this error. Using gdc (D compiler) I get this error message on my crunchbang debian linux machine:
gdc main.d fasta.d utilities.d
utilities.d:3: Error: module file is in file 'file.d' which cannot be read
import path[0] = /usr/include/d2/4.6/x86_64-linux-gnu
import path[1] = /usr/include/d2/4.6
utilities.d:3: Error: module file is in file 'file.d' which cannot be read
import path[0] = /usr/include/d2/4.6/x86_64-linux-gnu
import path[1] = /usr/include/d2/4.6
This is after freshly installing gdc with apt-get install.