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rfael0cm / RTIGER

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Segmentation fault in setupJulia() #2

Closed mnshgl0110 closed 3 years ago

mnshgl0110 commented 3 years ago

Hi Rafa,

I was able to load RTIGER correctly by installing Gviz manually (see here https://github.com/rfael0cm/RTIGER/issues/1). But, I am getting segmentation fault in setupJulia().

>  setupJulia()
Julia version 1.0.5 at location /srv/netscratch/dep_mercier/grp_schneeberger/software/julia-1.0.5/bin will be used.
Loading setup script for JuliaCall...

signal (11): Segmentation fault
in expression starting at /home/goel/R/x86_64-pc-linux-gnu-library/3.6/JuliaCall/julia/setup.jl:72
GetNewPage at /opt/share/software/build/R-3.5.1/src/main/memory.c:904
Rf_allocVector3 at /opt/share/software/build/R-3.5.1/src/main/memory.c:2539
Rf_ScalarInteger at /opt/share/software/build/R-3.5.1/src/main/../../src/include/Rinlinedfuns.h:984
__init__ at /home/goel/.julia/packages/RCall/Qzssx/src/setup.jl:192
unknown function (ip: 0x7ff6736df141)
jl_fptr_trampoline at /buildworker/worker/package_linux64/build/src/gf.c:1809
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2162
jl_apply at /buildworker/worker/package_linux64/build/src/julia.h:1537 [inlined]
jl_module_run_initializer at /buildworker/worker/package_linux64/build/src/toplevel.c:90
jl_init_restored_modules at /buildworker/worker/package_linux64/build/src/dump.c:2418
_include_from_serialized at ./loading.jl:633
_require_search_from_serialized at ./loading.jl:713
_require at ./loading.jl:937
require at ./loading.jl:858
require at ./loading.jl:853
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2162
jl_apply at /buildworker/worker/package_linux64/build/src/julia.h:1537 [inlined]
call_require at /buildworker/worker/package_linux64/build/src/toplevel.c:441 [inlined]
eval_import_path at /buildworker/worker/package_linux64/build/src/toplevel.c:476
jl_toplevel_eval_flex at /buildworker/worker/package_linux64/build/src/toplevel.c:671
jl_eval_module_expr at /buildworker/worker/package_linux64/build/src/toplevel.c:232
jl_toplevel_eval_flex at /buildworker/worker/package_linux64/build/src/toplevel.c:655
jl_parse_eval_all at /buildworker/worker/package_linux64/build/src/ast.c:838
jl_load at /buildworker/worker/package_linux64/build/src/toplevel.c:839
include at ./boot.jl:317 [inlined]
include_relative at ./loading.jl:1044
include at ./sysimg.jl:29
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2162
do_call at /buildworker/worker/package_linux64/build/src/interpreter.c:324
eval_value at /buildworker/worker/package_linux64/build/src/interpreter.c:430
eval_stmt_value at /buildworker/worker/package_linux64/build/src/interpreter.c:363 [inlined]
eval_body at /buildworker/worker/package_linux64/build/src/interpreter.c:682
jl_interpret_toplevel_thunk_callback at /buildworker/worker/package_linux64/build/src/interpreter.c:806
unknown function (ip: 0xfffffffffffffffe)
unknown function (ip: 0x7ff676f3f52f)
unknown function (ip: (nil))
jl_interpret_toplevel_thunk at /buildworker/worker/package_linux64/build/src/interpreter.c:815
jl_toplevel_eval_flex at /buildworker/worker/package_linux64/build/src/toplevel.c:805
jl_toplevel_eval_in at /buildworker/worker/package_linux64/build/src/builtins.c:622
jl_eval_string at /buildworker/worker/package_linux64/build/src/jlapi.c:95
juliacall_cmd at /tmp/RtmpdzknZd/R.INSTALL70521c0b7f20/JuliaCall/src/JuliaCall.cpp:54
_JuliaCall_juliacall_cmd at /tmp/RtmpdzknZd/R.INSTALL70521c0b7f20/JuliaCall/src/RcppExports.cpp:28
do_dotcall at /opt/share/software/build/R-3.6.1/src/main/dotcode.c:1252
bcEval at /opt/share/software/build/R-3.6.1/src/main/eval.c:6765
Rf_eval at /opt/share/software/build/R-3.6.1/src/main/eval.c:620
R_execClosure at /opt/share/software/build/R-3.6.1/src/main/eval.c:1780
Rf_applyClosure at /opt/share/software/build/R-3.6.1/src/main/eval.c:1706
bcEval at /opt/share/software/build/R-3.6.1/src/main/eval.c:6733
Rf_eval at /opt/share/software/build/R-3.6.1/src/main/eval.c:620
R_execClosure at /opt/share/software/build/R-3.6.1/src/main/eval.c:1780
Rf_applyClosure at /opt/share/software/build/R-3.6.1/src/main/eval.c:1706
bcEval at /opt/share/software/build/R-3.6.1/src/main/eval.c:6733
Rf_eval at /opt/share/software/build/R-3.6.1/src/main/eval.c:620
R_execClosure at /opt/share/software/build/R-3.6.1/src/main/eval.c:1780
Rf_applyClosure at /opt/share/software/build/R-3.6.1/src/main/eval.c:1706
bcEval at /opt/share/software/build/R-3.6.1/src/main/eval.c:6733
Rf_eval at /opt/share/software/build/R-3.6.1/src/main/eval.c:620
R_execClosure at /opt/share/software/build/R-3.6.1/src/main/eval.c:1780
Rf_applyClosure at /opt/share/software/build/R-3.6.1/src/main/eval.c:1706
bcEval at /opt/share/software/build/R-3.6.1/src/main/eval.c:6733
Rf_eval at /opt/share/software/build/R-3.6.1/src/main/eval.c:620
R_execClosure at /opt/share/software/build/R-3.6.1/src/main/eval.c:1780
Rf_applyClosure at /opt/share/software/build/R-3.6.1/src/main/eval.c:1706
bcEval at /opt/share/software/build/R-3.6.1/src/main/eval.c:6733
Rf_eval at /opt/share/software/build/R-3.6.1/src/main/eval.c:620
R_execClosure at /opt/share/software/build/R-3.6.1/src/main/eval.c:1780
Rf_applyClosure at /opt/share/software/build/R-3.6.1/src/main/eval.c:1706
bcEval at /opt/share/software/build/R-3.6.1/src/main/eval.c:6733
Rf_eval at /opt/share/software/build/R-3.6.1/src/main/eval.c:620
R_execClosure at /opt/share/software/build/R-3.6.1/src/main/eval.c:1780
Rf_applyClosure at /opt/share/software/build/R-3.6.1/src/main/eval.c:1706
bcEval at /opt/share/software/build/R-3.6.1/src/main/eval.c:6733
Rf_eval at /opt/share/software/build/R-3.6.1/src/main/eval.c:620
R_execClosure at /opt/share/software/build/R-3.6.1/src/main/eval.c:1780
Rf_applyClosure at /opt/share/software/build/R-3.6.1/src/main/eval.c:1706
Rf_eval at /opt/share/software/build/R-3.6.1/src/main/eval.c:743
Rf_ReplIteration at /opt/share/software/build/R-3.6.1/src/main/main.c:260
R_ReplConsole at /opt/share/software/build/R-3.6.1/src/main/main.c:310
run_Rmainloop at /opt/share/software/build/R-3.6.1/src/main/main.c:1086
main at /opt/share/software/build/R-3.6.1/src/main/Rmain.c:29
__libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
_start at /opt/share/software/packages/R-3.6.1-debian-9/lib/R/bin/exec/R (unknown line)
Allocations: 4158824 (Pool: 4158420; Big: 404); GC: 6
Segmentation fault
Sophia755 commented 3 years ago

It seems to be related to this error in the JuliaCall Package: https://discourse.julialang.org/t/loading-setup-script-for-juliacall-in-r-not-working/51285/6 The suggested solution is: Delete the "user/.julia/registries/General/" folder and than run in Julia:

using Pkg; Pkg.add("Suppressor"); Pkg.add("RCall"); 
using Suppressor; using RCall;