sf

A number of packages use it as dependency and there might be error such as this,

Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared object '/rds/user/jhz22/hpc-work/R/sf/libs/sf.so':
  /rds/user/jhz22/hpc-work/R/sf/libs/sf.so: undefined symbol: GEOSSTRtree_nearest_generic_r
Calls: <Anonymous> ... asNamespace -> loadNamespace -> library.dynam -> dyn.load
Execution halted
 

We can get away with this,

module load geos-3.6.2-gcc-5.4.0-vejexvy
module load gcc/6
Rscript -e "install.packages('sf')"
 

1.0-10/11/12

We have seen error

Error: package or namespace load failed for ‘sf' in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/rds/user/jhz22/hpc-work/R/00LOCK-sf-10/00new/sf/libs/sf.so':
  /rds/user/jhz22/hpc-work/R/00LOCK-sf-10/00new/sf/libs/sf.so: undefined symbol: _Z16CPL_gdalmdiminfoN4Rcpp6VectorILi16ENS_15PreserveStorageEEES2_S2_S2_
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/rds/user/jhz22/hpc-work/R/sf'
* restoring previous ‘/rds/user/jhz22/hpc-work/R/sf'
 

though they generate the same sf/src/Makevars as 1.0-9 which is installed successfully.

The error is actually due to Rcpp and after its reinstallation the loading is OK.