EXCAVATOR error - Missing F4R.so file

Question

[matthew.1.davies]

Hi

I'm trying to run EXCAVATOR but I get the following error.

Error in dyn.load(paste(Program_Folder, "/lib/F77/F4R.so", sep = "")) :
  unable to load shared object '/scratch/molcarc/mdavies/colrec/EXCAVATOR/EXCAVATOR_Package_v2.2/EXCAVATOR/lib/F77/F4R.so':
  /scratch/molcarc/mdavies/colrec/EXCAVATOR/EXCAVATOR_Package_v2.2/EXCAVATOR/lib/F77/F4R.so: cannot open shared object file: No such file or directory

The file (presumably a shared library file) is called by the MakeReadCount.R and NeoMap.R scripts

dyn.load(paste(Program_Folder,"/lib/F77/F4R.so",sep=""))

but I can't find it in either version of the program. Can anyone suggest where I'm going wrong?

Many thanks

Matt

Answer 1

[alison.meynert]

I ran into the same problem just now. It seems to be due to using a new version of R. Try re-compiling the two Fortran libraries.

cd $EXCAVATOR_HOME/lib/F77
rm *.so *.o
R CMD SHLIB F4R.f
R CMD SHLIB FastJointSLMLibraryI.f