RCall vscode REPL crash

Tooling VS Code
1

I was trying to using RCall in VSCode’s Julia REPL. It crashes.

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image858×96 3.88 KB
But if I start a REPL from terminal it works fine.
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image852×70 2.44 KB

(Note: the rfunctions.jl below only has one line of using RCall so that I can capture the error. Since if I did not put it into a scripts, the VSCode’s Julia REPL will only flashes the error and quit.)

FATAL ERROR: Symbol "ccalllib_libR.so499"not found
signal (6): Aborted
in expression starting at /Extension_HDD1/src/rfunctions.jl:6 
gsignal at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
abort at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
addModule at /buildworker/worker/package_linux64/build/src/jitlayers.cpp:640
jl_add_to_ee at /buildworker/worker/package_linux64/build/src/jitlayers.cpp:893 [inlined]
jl_add_to_ee at /buildworker/worker/package_linux64/build/src/jitlayers.cpp:955
jl_add_to_ee at /buildworker/worker/package_linux64/build/src/jitlayers.cpp:977 [inlined]
_jl_compile_codeinst at /buildworker/worker/package_linux64/build/src/jitlayers.cpp:126
jl_generate_fptr at /buildworker/worker/package_linux64/build/src/jitlayers.cpp:302
jl_compile_method_internal at /buildworker/worker/package_linux64/build/src/gf.c:1964
gen_cfun_wrapper at /buildworker/worker/package_linux64/build/src/codegen.cpp:4025
emit_cfunction at /buildworker/worker/package_linux64/build/src/codegen.cpp:4611 [inlined]
emit_expr at /buildworker/worker/package_linux64/build/src/codegen.cpp:3651
emit_ssaval_assign at /buildworker/worker/package_linux64/build/src/codegen.cpp:3339
emit_stmtpos at /buildworker/worker/package_linux64/build/src/codegen.cpp:3533 [inlined]
emit_function at /buildworker/worker/package_linux64/build/src/codegen.cpp:6085
jl_emit_code at /buildworker/worker/package_linux64/build/src/codegen.cpp:6431
jl_emit_codeinst at /buildworker/worker/package_linux64/build/src/codegen.cpp:6465
_jl_compile_codeinst at /buildworker/worker/package_linux64/build/src/jitlayers.cpp:97
jl_generate_fptr at /buildworker/worker/package_linux64/build/src/jitlayers.cpp:302
jl_compile_method_internal at /buildworker/worker/package_linux64/build/src/gf.c:1964
jl_compile_method_internal at /buildworker/worker/package_linux64/build/src/gf.c:1919 [inlined]
_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2224 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2398
jl_apply at /buildworker/worker/package_linux64/build/src/julia.h:1690 [inlined]
jl_module_run_initializer at /buildworker/worker/package_linux64/build/src/toplevel.c:74
jl_init_restored_modules at /buildworker/worker/package_linux64/build/src/dump.c:2544
_include_from_serialized at ./loading.jl:697
_require_from_serialized at ./loading.jl:749
_require at ./loading.jl:1040
require at ./loading.jl:928
require at ./loading.jl:923
_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2214 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2398
jl_apply at /buildworker/worker/package_linux64/build/src/julia.h:1690 [inlined]
call_require at /buildworker/worker/package_linux64/build/src/toplevel.c:425 [inlined]
eval_import_path at /buildworker/worker/package_linux64/build/src/toplevel.c:462
jl_toplevel_eval_flex at /buildworker/worker/package_linux64/build/src/toplevel.c:682
jl_eval_module_expr at /buildworker/worker/package_linux64/build/src/toplevel.c:197
jl_toplevel_eval_flex at /buildworker/worker/package_linux64/build/src/toplevel.c:666
jl_parse_eval_all at /buildworker/worker/package_linux64/build/src/ast.c:913
jl_load_rewrite at /buildworker/worker/package_linux64/build/src/toplevel.c:914
include at ./Base.jl:380
include at ./Base.jl:368
_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2214 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2398
jl_apply at /buildworker/worker/package_linux64/build/src/julia.h:1690 [inlined]
do_call at /buildworker/worker/package_linux64/build/src/interpreter.c:117
eval_value at /buildworker/worker/package_linux64/build/src/interpreter.c:206
eval_stmt_value at /buildworker/worker/package_linux64/build/src/interpreter.c:157 [inlined]
eval_body at /buildworker/worker/package_linux64/build/src/interpreter.c:566
eval_body at /buildworker/worker/package_linux64/build/src/interpreter.c:492
jl_interpret_toplevel_thunk at /buildworker/worker/package_linux64/build/src/interpreter.c:660
jl_toplevel_eval_flex at /buildworker/worker/package_linux64/build/src/toplevel.c:840
jl_toplevel_eval_in at /buildworker/worker/package_linux64/build/src/toplevel.c:883
eval at ./boot.jl:331 [inlined]
eval at ./client.jl:467
_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2214 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2398
top-level scope at ./none:3
jl_toplevel_eval_flex at /buildworker/worker/package_linux64/build/src/toplevel.c:834
jl_toplevel_eval_flex at /buildworker/worker/package_linux64/build/src/toplevel.c:790
jl_toplevel_eval_in at /buildworker/worker/package_linux64/build/src/toplevel.c:883
eval at ./boot.jl:331
_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2214 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2398
exec_options at ./client.jl:272
_start at ./client.jl:506
jfptr__start_43701.clone_1 at /home/software/julia-1.5.0/lib/julia/sys.so (unknown line)
_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2214 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2398
jl_apply at /buildworker/worker/package_linux64/build/ui/../src/julia.h:1690 [inlined]
true_main at /buildworker/worker/package_linux64/build/ui/repl.c:106
main at /buildworker/worker/package_linux64/build/ui/repl.c:227
__libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
_start at /home/software/julia-1.5.0/bin/julia (unknown line)
Allocations: 9988745 (Pool: 9984292; Big: 4453); GC: 11
1 Like
2

What’s your platform? I am experiencing a similar issue on Mac (stackoverflow post r - FATAL ERROR in JuliaCall: Symbol "ccalllib_libR.dylib74"not found - Stack Overflow).

3

I am using VSCode on Mac to remote use Julia and RCall from a Ubuntu system.

4

Can you try directly from terminal just to discard this being a VSCode error?

5

I think so that only happened to me using VSCode. Since then I switched to use tmux/nvim setup. I don’t have any issue.

6

For my similar issue I ended up rebuilding everything Pkg.build(“RCall”) and rebuilding all packages from R side (specially JuliaCall). That fixed it but idk if it was plain luck.

7

Hey there,
I happen to have the same problem.

I’m using a remote connection to a Centos machine with VSCode.

I can successfully call RCall in the regular REPL that’s activated when typing julia (double-checked this both in VSCode and Pycharm, though it shouldn’t matter).
But, when I try to execute the line using RCall through the Julia REPL by pressing ctrl+enter on that line, I get errors similar to those @Donut_Meepo reported:

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image1923×755 137 KB

I’m using Julia 1.52.

Thanks!

8

Can you compare ENV in a Julia REPL outside of VSCode and inside? It’s likely the PATH entry or something related to R is different.