Rscript runGeneral.r error

Open rogeorg2 opened this issue 2 years ago • 0 comments

Hello,

I am trying to filter ancient whole genome data using the --rescale option with mapDamage2. All the plotting output files are generated fine, however an error appears for the statistical estimation step. The error message in the progression information reads:

mapdamage.rscript INFO Error in dyn.load("/private/var/folders/p8/m48gkzgj4gs33b4t1c_d6vs8s2hj1y/T/RtmpVmjTG6/sourceCpp-x86_64-apple-darwin20-1.0.11/sourcecpp_1496333620720/sourceCpp_2.so") : mapdamage.rscript INFO unable to load shared object '/private/var/folders/p8/m48gkzgj4gs33b4t1c_d6vs8s2hj1y/T/RtmpVmjTG6/sourceCpp-x86_64-apple-darwin20-1.0.11/sourcecpp_1496333620720/sourceCpp_2.so': mapdamage.rscript INFO dlopen(/private/var/folders/p8/m48gkzgj4gs33b4t1c_d6vs8s2hj1y/T/RtmpVmjTG6/sourceCpp-x86_64-apple-darwin20-1.0.11/sourcecpp_1496333620720/sourceCpp_2.so, 0x0006): symbol not found in flat namespace '__ZNKSt5ctypeIcE13_M_widen_initEv'

The final error message reads: mapdamage.rscript ERROR Command returned error 1: 'Rscript runGeneral.r

I have tried reinstalling the required R packages, and have tried manually installing sourceCpp_2.so. When I do so, an error message appears saying that I do not have the correct version of R required for this package, yet my R is fully up to date and I cannot find which version sourceCpp_2.so requires.

I am confused whether sourceCpp_2.so is the issue, or whether there are issues with the c++ extension or Rcpp package. I have never used mapDamage and am new to using these kinds of programs, so any help would be appreciated!

Thanks!!

Nov 06 '23 19:11 rogeorg2