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segfault with R-devel #469

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bbolker opened this issue Nov 22, 2022 · 0 comments
Closed

segfault with R-devel #469

bbolker opened this issue Nov 22, 2022 · 0 comments

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@bbolker
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bbolker commented Nov 22, 2022

I'm sure I'm doing something silly, but don't know what it is.

A fresh install of Julia via apt-get install on PopOS! 22.04 (if it would be useful I could install 1.8.3 ...)

Fresh install of RCall, just did Pkg.build("RCall").

R is configured with --enable-R-shlib --with-blas --with-lapack

R Under development (unstable) (2022-11-21 r83373) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

Any ideas ...?

julia> import RCall

signal (11): Segmentation fault
in expression starting at REPL[1]:1
Rf_install at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/names.c:1255
R_initMethodDispatch at /home/bolker/R/r-build/src/library/methods/src/../../../../../r-devel/src/library/methods/src/methods_list_dispatch.c:159
R_initMethodDispatch at /home/bolker/R/r-build/src/library/methods/src/../../../../../r-devel/src/library/methods/src/methods_list_dispatch.c:156
R_doDotCall at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/dotcode.c:868
bcEval at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:7720
Rf_eval at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:786
R_execClosure at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:1956
Rf_applyClosure at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:1882
bcEval at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:7132
Rf_eval at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:786
R_execClosure at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:1956
Rf_applyClosure at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:1882
bcEval at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:7132
Rf_eval at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:786
forcePromise at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:606
FORCE_PROMISE at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:5185 [inlined]
getvar at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:5226
bcEval at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:6916
Rf_eval at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:786
forcePromise at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:606
FORCE_PROMISE at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:5185 [inlined]
getvar at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:5226
bcEval at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:6916
Rf_eval at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:786
forcePromise at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:606
FORCE_PROMISE at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:5185 [inlined]
getvar at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:5226
bcEval at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:6916
Rf_eval at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:786
forcePromise at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:606
FORCE_PROMISE at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:5185 [inlined]
getvar at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:5226
bcEval at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:6916
Rf_eval at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:786
R_execClosure at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:1956
Rf_applyClosure at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:1882
bcEval at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:7132
Rf_eval at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:786
R_execClosure at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:1956
Rf_applyClosure at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:1882
bcEval at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:7132
Rf_eval at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:786
R_execClosure at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:1956
Rf_applyClosure at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:1882
bcEval at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:7132
Rf_eval at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:786
R_execClosure at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:1956
Rf_applyClosure at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:1882
bcEval at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:7132
Rf_eval at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:786
R_execClosure at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:1956
Rf_applyClosure at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:1882
bcEval at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:7132
Rf_eval at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:786
R_execClosure at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:1956
Rf_applyClosure at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:1882
bcEval at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:7132
Rf_eval at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:786
forcePromise at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:606
FORCE_PROMISE at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:5185 [inlined]
getvar at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:5226
bcEval at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:6916
Rf_eval at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:786
forcePromise at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:606
FORCE_PROMISE at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:5185 [inlined]
getvar at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:5226
bcEval at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:6916
Rf_eval at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:786
forcePromise at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:606
FORCE_PROMISE at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:5185 [inlined]
getvar at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:5226
bcEval at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:6916
Rf_eval at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:786
forcePromise at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:606
FORCE_PROMISE at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:5185 [inlined]
getvar at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:5226
bcEval at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:6916
Rf_eval at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:786
R_execClosure at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:1956
Rf_applyClosure at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:1882
bcEval at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:7132
Rf_eval at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:786
R_execClosure at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:1956
Rf_applyClosure at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:1882
bcEval at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:7132
Rf_eval at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:786
R_execClosure at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:1956
Rf_applyClosure at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:1882
bcEval at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:7132
Rf_eval at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:786
R_execClosure at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:1956
Rf_applyClosure at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:1882
bcEval at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:7132
Rf_eval at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:786
R_execClosure at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:1956
Rf_applyClosure at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:1882
bcEval at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:7132
Rf_eval at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:786
forcePromise at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:606
FORCE_PROMISE at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:5185 [inlined]
getvar at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:5226
bcEval at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:6916
Rf_eval at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:786
forcePromise at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:606
FORCE_PROMISE at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:5185 [inlined]
getvar at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:5226
bcEval at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:6916
Rf_eval at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:786
forcePromise at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:606
FORCE_PROMISE at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:5185 [inlined]
getvar at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:5226
bcEval at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:6916
Rf_eval at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:786
forcePromise at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:606
FORCE_PROMISE at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:5185 [inlined]
getvar at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:5226
bcEval at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:6916
Rf_eval at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:786
R_execClosure at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:1956
Rf_applyClosure at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:1882
bcEval at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:7132
Rf_eval at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:786
R_execClosure at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:1956
Rf_applyClosure at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:1882
bcEval at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:7132
Rf_eval at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:786
R_execClosure at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:1956
Rf_applyClosure at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:1882
bcEval at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:7132
Rf_eval at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:786
R_execClosure at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:1956
Rf_applyClosure at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:1882
bcEval at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:7132
Rf_eval at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:786
R_execClosure at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:1956
Rf_applyClosure at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:1882
Rf_eval at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:909
Rf_evalList at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:3117
Rf_eval at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:880
do_if at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:2275
Rf_eval at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:861
Rf_eval at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:861
do_begin at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:2567
Rf_eval at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:861
R_execClosure at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:1956
Rf_applyClosure at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:1882
Rf_eval at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/eval.c:909
setup_Rmainloop at /home/bolker/R/r-build/src/main/../../../r-devel/src/main/main.c:1061
initEmbeddedR at /home/bolker/.julia/packages/RCall/Wyd74/src/setup.jl:151
__init__ at /home/bolker/.julia/packages/RCall/Wyd74/src/setup.jl:186
unknown function (ip: 0x7f96ead0cac4)
_jl_invoke at /cache/build/default-amdci4-6/julialang/julia-release-1-dot-8/src/gf.c:2367 [inlined]
ijl_apply_generic at /cache/build/default-amdci4-6/julialang/julia-release-1-dot-8/src/gf.c:2549
jl_apply at /cache/build/default-amdci4-6/julialang/julia-release-1-dot-8/src/julia.h:1839 [inlined]
jl_module_run_initializer at /cache/build/default-amdci4-6/julialang/julia-release-1-dot-8/src/toplevel.c:75
ijl_init_restored_modules at /cache/build/default-amdci4-6/julialang/julia-release-1-dot-8/src/dump.c:2602
_include_from_serialized at ./loading.jl:831
_require_search_from_serialized at ./loading.jl:1039
_require at ./loading.jl:1315
_require_prelocked at ./loading.jl:1200
macro expansion at ./loading.jl:1180 [inlined]
macro expansion at ./lock.jl:223 [inlined]
require at ./loading.jl:1144
jfptr_require_47742.clone_1 at /usr/lib/julia/sys.so (unknown line)
_jl_invoke at /cache/build/default-amdci4-6/julialang/julia-release-1-dot-8/src/gf.c:2367 [inlined]
ijl_apply_generic at /cache/build/default-amdci4-6/julialang/julia-release-1-dot-8/src/gf.c:2549
jl_apply at /cache/build/default-amdci4-6/julialang/julia-release-1-dot-8/src/julia.h:1839 [inlined]
call_require at /cache/build/default-amdci4-6/julialang/julia-release-1-dot-8/src/toplevel.c:462 [inlined]
eval_import_path at /cache/build/default-amdci4-6/julialang/julia-release-1-dot-8/src/toplevel.c:499
jl_toplevel_eval_flex at /cache/build/default-amdci4-6/julialang/julia-release-1-dot-8/src/toplevel.c:778
jl_toplevel_eval_flex at /cache/build/default-amdci4-6/julialang/julia-release-1-dot-8/src/toplevel.c:850
ijl_toplevel_eval_in at /cache/build/default-amdci4-6/julialang/julia-release-1-dot-8/src/toplevel.c:965
eval at ./boot.jl:368 [inlined]
eval_user_input at /cache/build/default-amdci4-6/julialang/julia-release-1-dot-8/usr/share/julia/stdlib/v1.8/REPL/src/REPL.jl:151
repl_backend_loop at /cache/build/default-amdci4-6/julialang/julia-release-1-dot-8/usr/share/julia/stdlib/v1.8/REPL/src/REPL.jl:247
start_repl_backend at /cache/build/default-amdci4-6/julialang/julia-release-1-dot-8/usr/share/julia/stdlib/v1.8/REPL/src/REPL.jl:232
#run_repl#47 at /cache/build/default-amdci4-6/julialang/julia-release-1-dot-8/usr/share/julia/stdlib/v1.8/REPL/src/REPL.jl:369
run_repl at /cache/build/default-amdci4-6/julialang/julia-release-1-dot-8/usr/share/julia/stdlib/v1.8/REPL/src/REPL.jl:355
jfptr_run_repl_64841.clone_1 at /usr/lib/julia/sys.so (unknown line)
_jl_invoke at /cache/build/default-amdci4-6/julialang/julia-release-1-dot-8/src/gf.c:2367 [inlined]
ijl_apply_generic at /cache/build/default-amdci4-6/julialang/julia-release-1-dot-8/src/gf.c:2549
#967 at ./client.jl:419
jfptr_YY.967_30403.clone_1 at /usr/lib/julia/sys.so (unknown line)
_jl_invoke at /cache/build/default-amdci4-6/julialang/julia-release-1-dot-8/src/gf.c:2367 [inlined]
ijl_apply_generic at /cache/build/default-amdci4-6/julialang/julia-release-1-dot-8/src/gf.c:2549
jl_apply at /cache/build/default-amdci4-6/julialang/julia-release-1-dot-8/src/julia.h:1839 [inlined]
jl_f__call_latest at /cache/build/default-amdci4-6/julialang/julia-release-1-dot-8/src/builtins.c:774
#invokelatest#2 at ./essentials.jl:729 [inlined]
invokelatest at ./essentials.jl:726 [inlined]
run_main_repl at ./client.jl:404
exec_options at ./client.jl:318
_start at ./client.jl:522
jfptr__start_56736.clone_1 at /usr/lib/julia/sys.so (unknown line)
_jl_invoke at /cache/build/default-amdci4-6/julialang/julia-release-1-dot-8/src/gf.c:2367 [inlined]
ijl_apply_generic at /cache/build/default-amdci4-6/julialang/julia-release-1-dot-8/src/gf.c:2549
jl_apply at /cache/build/default-amdci4-6/julialang/julia-release-1-dot-8/src/julia.h:1839 [inlined]
true_main at /cache/build/default-amdci4-6/julialang/julia-release-1-dot-8/src/jlapi.c:575
jl_repl_entrypoint at /cache/build/default-amdci4-6/julialang/julia-release-1-dot-8/src/jlapi.c:719
main at julia (unknown line)
unknown function (ip: 0x7f96ec429d8f)
__libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
unknown function (ip: 0x401098)
Allocations: 3870962 (Pool: 3868736; Big: 2226); GC: 5
Segmentation fault (core dumped)
@bbolker bbolker closed this as completed May 8, 2024
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