RCall having FATAL ERROR during precompilation

[tomouellette]

julia> using RCall
[ Info: Precompiling RCall [6f49c342-dc21-5d91-9882-a32aef131414]
FATAL ERROR: Symbol "ccalllib_libR.so693"not found
signal (6): Aborted
in expression starting at REPL[7]:1

[simonbyrne]

What version of Julia & RCall are you using? What OS are you using? How did you install R?

[tomouellette]

Versions: Julia v1.5.3, R 4.0.3, RCall most recent
OS: Linux Ubuntu - running on a Cluster

Both R and Julia installed from most recent stable builds (tars from respective sources)

Oddly when I build RCall it calls Conda,

Building Conda → ~/.julia/packages/Conda/x5ml4/deps/build.log Building RCall → ~/.julia/packages/RCall/eRsxl/deps/build.log

And ENV["R_HOME"] and ENV["LD_LIBRARY_PATH"] are set correctly.

Here is the full output:

[ Info: Precompiling RCall [6f49c342-dc21-5d91-9882-a32aef131414]
FATAL ERROR: Symbol "ccalllib_libR.so741"not found
signal (6): Aborted
in expression starting at REPL[6]:1
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:4068
emit_cfunction at /buildworker/worker/package_linux64/build/src/codegen.cpp:4654 [inlined]
emit_expr at /buildworker/worker/package_linux64/build/src/codegen.cpp:3694
emit_ssaval_assign at /buildworker/worker/package_linux64/build/src/codegen.cpp:3339
emit_stmtpos at /buildworker/worker/package_linux64/build/src/codegen.cpp:3576 [inlined]
emit_function at /buildworker/worker/package_linux64/build/src/codegen.cpp:6110
jl_emit_code at /buildworker/worker/package_linux64/build/src/codegen.cpp:6463
jl_emit_codeinst at /buildworker/worker/package_linux64/build/src/codegen.cpp:6497
_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:2541
_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_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
eval_user_input at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.5/REPL/src/REPL.jl:134
repl_backend_loop at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.5/REPL/src/REPL.jl:195
start_repl_backend at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.5/REPL/src/REPL.jl:180
#run_repl#37 at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.5/REPL/src/REPL.jl:292
run_repl at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.5/REPL/src/REPL.jl:288
_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2231 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2398
#807 at ./client.jl:399
jfptr_YY.807_45002.clone_1 at /.mounts/labs/awadallalab/private/touellette/julia-1.5.3/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/src/julia.h:1690 [inlined]
do_apply at /buildworker/worker/package_linux64/build/src/builtins.c:655
jl_f__apply_latest at /buildworker/worker/package_linux64/build/src/builtins.c:705
#invokelatest#1 at ./essentials.jl:710 [inlined]
invokelatest at ./essentials.jl:709 [inlined]
run_main_repl at ./client.jl:383
exec_options at ./client.jl:313
_start at ./client.jl:506
jfptr__start_53898.clone_1 at /.mounts/labs/awadallalab/private/touellette/julia-1.5.3/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 /./.mounts/labs/awadallalab/private/touellette/julia-1.5.3/bin/julia (unknown line)
Allocations: 20012586 (Pool: 20003698; Big: 8888); GC: 26
Aborted```