I've been having some issues getting R to run properly on the shared cluster at my institution , where i don't have root access. Some things will work but it gets tricky when i need to install packages etc. The current issue i'm trying to trouble shoot is the following error when trying to load the caret package:
Loading required package: lattice
Loading required package: ggplot2
Error: package or namespace load failed for ‘ggplot2’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/cifs/hariri-long/Scripts/Tools/R/packages/rlang/libs/rlang.so':
/cifs/hariri-long/Scripts/Tools/R/packages/rlang/libs/rlang.so: undefined symbol: R_removeVarFromFrame
Error: package ‘ggplot2’ could not be loaded
Execution halted
I found this page suggesting i install rlang as follows:
> install.packages("rlang",type="source")
Installing package into ‘/cifs/hariri-long/Scripts/Tools/R/packages’
(as ‘lib’ is unspecified)
--- Please select a CRAN mirror for use in this session ---
Error: .onLoad failed in loadNamespace() for 'tcltk', details:
call: fun(libname, pkgname)
error: Can't find a usable init.tcl in the following directories:
/usr/share/tcl8.5 ./lib/tcl8.5 ./lib/tcl8.5 ./library ./library ./tcl8.5.13/library ./tcl8.5.13/library
but i get the above tcl error. since i've seen this in other threads:
> capabilities("tcltk")
tcltk
TRUE
it looks like tcl on my system is 8.6, but i don't know how to tell R to look for that version.
$ whereis tcl
tcl: /usr/lib64/tcl8.6 /usr/include/tcl.h /usr/share/tcl8.6
$ which R
/opt/apps/rhel7/R-3.6.0/bin/R
Any ideas? The OS is CentOS 8. Thanks!
I ended up deciding to try using a more recent R version (4.1.1) to solve this issue. I was hesitant to do this at first because I have run into issues with availability / compatibility of packages I need in more recent R versions, but I wasn't getting anywhere troubleshooting this issue otherwise. I figured that since TCL 8.6 is what was installed on the system, a newer version of R might be able to work with it, and seems i was right, since I got past the first error I was having when I switched.
I did get a new error regarding an issue loading the shared library Libtk8.6.so. So I downloaded the .so file from here and unpacked it to my home directory using rpm2cpio (i don't have root access so i can't just use yum install etc). After that i just had to re-install all my packages for the new R version and it worked!