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Segmentation Fault using R 4.3.0 #195

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karimn opened this issue May 10, 2023 · 3 comments
Open

Segmentation Fault using R 4.3.0 #195

karimn opened this issue May 10, 2023 · 3 comments

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@karimn
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karimn commented May 10, 2023 •
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Session Info

Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────
setting value
version R version 4.3.0 (2023-04-21)
os Pop!_OS 22.04 LTS
system x86_64, linux-gnu
ui X11
language en_US:en
collate en_US.UTF-8
ctype en_US.UTF-8
tz America/New_York
date 2023-05-10
pandoc 2.9.2.1 @ /usr/bin/pandoc

─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
! package * version date (UTC) lib source
P cachem 1.0.8 2023-05-01 [?] CRAN (R 4.3.0)
P callr 3.7.3 2022-11-02 [?] CRAN (R 4.3.0)
P cli 3.6.1 2023-03-23 [?] CRAN (R 4.3.0)
P crayon 1.5.2 2022-09-29 [?] CRAN (R 4.3.0)
P devtools 2.4.5 2022-10-11 [?] CRAN (R 4.3.0)
P digest 0.6.31 2022-12-11 [?] CRAN (R 4.3.0)
P ellipsis 0.3.2 2021-04-29 [?] CRAN (R 4.3.0)
P fastmap 1.1.1 2023-02-24 [?] CRAN (R 4.3.0)
P fs 1.6.2 2023-04-25 [?] CRAN (R 4.3.0)
P glue 1.6.2 2022-02-24 [?] CRAN (R 4.3.0)
P htmltools 0.5.5 2023-03-23 [?] CRAN (R 4.3.0)
P htmlwidgets 1.6.2 2023-03-17 [?] CRAN (R 4.3.0)
P httpuv 1.6.10 2023-05-08 [?] CRAN (R 4.3.0)
P later 1.3.1 2023-05-02 [?] CRAN (R 4.3.0)
P lifecycle 1.0.3 2022-10-07 [?] CRAN (R 4.3.0)
P magrittr 2.0.3 2022-03-30 [?] CRAN (R 4.3.0)
P memoise 2.0.1 2021-11-26 [?] CRAN (R 4.3.0)
P mime 0.12 2021-09-28 [?] CRAN (R 4.3.0)
P miniUI 0.1.1.1 2018-05-18 [?] CRAN (R 4.3.0)
P pkgbuild 1.4.0 2022-11-27 [?] CRAN (R 4.3.0)
P pkgload 1.3.2 2022-11-16 [?] CRAN (R 4.3.0)
P prettyunits 1.1.1 2020-01-24 [?] CRAN (R 4.3.0)
P processx 3.8.1 2023-04-18 [?] CRAN (R 4.3.0)
P profvis 0.3.8 2023-05-02 [?] CRAN (R 4.3.0)
P promises 1.2.0.1 2021-02-11 [?] CRAN (R 4.3.0)
P ps 1.7.5 2023-04-18 [?] CRAN (R 4.3.0)
P purrr 1.0.1 2023-01-10 [?] CRAN (R 4.3.0)
P R6 2.5.1 2021-08-19 [?] CRAN (R 4.3.0)
P Rcpp 1.0.10 2023-01-22 [?] CRAN (R 4.3.0)
P remotes 2.4.2 2021-11-30 [?] CRAN (R 4.3.0)
renv 0.17.3 2023-04-06 [1] CRAN (R 4.3.0)
P rlang 1.1.1 2023-04-28 [?] CRAN (R 4.3.0)
P sessioninfo 1.2.2 2021-12-06 [?] CRAN (R 4.3.0)
P shiny 1.7.4 2022-12-15 [?] CRAN (R 4.3.0)
P stringi 1.7.12 2023-01-11 [?] CRAN (R 4.3.0)
P stringr 1.5.0 2022-12-02 [?] CRAN (R 4.3.0)
P urlchecker 1.0.1 2021-11-30 [?] CRAN (R 4.3.0)
P usethis 2.1.6 2022-05-25 [?] CRAN (R 4.3.0)
P vctrs 0.6.2 2023-04-19 [?] CRAN (R 4.3.0)
P xtable 1.8-4 2019-04-21 [?] CRAN (R 4.3.0)
P yaml 2.3.7 2023-01-23 [?] CRAN (R 4.3.0)

[1] /media/karim/Code-Drive/karimn-code/test/renv/library/R-4.3/x86_64-pc-linux-gnu
[2] /home/karim/.cache/R/renv/sandbox/R-4.3/x86_64-pc-linux-gnu/d4a79710

P ── Loaded and on-disk path mismatch.

> JuliaCall::julia_call("x = 10")
Julia version 1.9.0 at location /home/karim/.julia/juliaup/julia-1.9.0+0.x64.linux.gnu/bin will be used.
Loading setup script for JuliaCall...

[863586] signal (11.1): Segmentation fault
in expression starting at /home/karim/.cache/R/renv/cache/v5/R-4.3/x86_64-pc-linux-gnu/JuliaCall/0.17.5/3fc7235465a350731873abfe58fed1b9/JuliaCall/julia/setup.jl:80
GetNewPage at /home/karim/R-builds/R-4.2.0/src/main/memory.c:993
Rf_allocVector3 at /home/karim/R-builds/R-4.2.0/src/main/memory.c:2665
Rf_ScalarInteger at /home/karim/R-builds/R-4.2.0/src/main/../../src/include/Rinlinedfuns.h:1002
__init__ at /home/karim/.julia/packages/RCall/LWzAQ/src/setup.jl:189
jfptr___init___617 at /home/karim/.julia/compiled/v1.9/RCall/8GFyb_fQokw.so (unknown line)
_jl_invoke at /cache/build/default-amdci4-0/julialang/julia-release-1-dot-9/src/gf.c:2758 [inlined]
ijl_apply_generic at /cache/build/default-amdci4-0/julialang/julia-release-1-dot-9/src/gf.c:2940
jl_apply at /cache/build/default-amdci4-0/julialang/julia-release-1-dot-9/src/julia.h:1879 [inlined]
jl_module_run_initializer at /cache/build/default-amdci4-0/julialang/julia-release-1-dot-9/src/toplevel.c:75
ijl_init_restored_modules at /cache/build/default-amdci4-0/julialang/julia-release-1-dot-9/src/module.c:982
register_restored_modules at ./loading.jl:1074
_include_from_serialized at ./loading.jl:1020
_require_search_from_serialized at ./loading.jl:1471
_require at ./loading.jl:1748
_require_prelocked at ./loading.jl:1625
macro expansion at ./loading.jl:1613 [inlined]
macro expansion at ./lock.jl:267 [inlined]
require at ./loading.jl:1576
jfptr_require_38136.clone_1 at /home/karim/.julia/juliaup/julia-1.9.0+0.x64.linux.gnu/lib/julia/sys.so (unknown line)
_jl_invoke at /cache/build/default-amdci4-0/julialang/julia-release-1-dot-9/src/gf.c:2758 [inlined]
ijl_apply_generic at /cache/build/default-amdci4-0/julialang/julia-release-1-dot-9/src/gf.c:2940
jl_apply at /cache/build/default-amdci4-0/julialang/julia-release-1-dot-9/src/julia.h:1879 [inlined]
call_require at /cache/build/default-amdci4-0/julialang/julia-release-1-dot-9/src/toplevel.c:466 [inlined]
eval_import_path at /cache/build/default-amdci4-0/julialang/julia-release-1-dot-9/src/toplevel.c:503
jl_toplevel_eval_flex at /cache/build/default-amdci4-0/julialang/julia-release-1-dot-9/src/toplevel.c:731
jl_eval_module_expr at /cache/build/default-amdci4-0/julialang/julia-release-1-dot-9/src/toplevel.c:203 [inlined]
jl_toplevel_eval_flex at /cache/build/default-amdci4-0/julialang/julia-release-1-dot-9/src/toplevel.c:715
jl_toplevel_eval_flex at /cache/build/default-amdci4-0/julialang/julia-release-1-dot-9/src/toplevel.c:856
ijl_toplevel_eval_in at /cache/build/default-amdci4-0/julialang/julia-release-1-dot-9/src/toplevel.c:971
eval at ./boot.jl:370 [inlined]
include_string at ./loading.jl:1864
_jl_invoke at /cache/build/default-amdci4-0/julialang/julia-release-1-dot-9/src/gf.c:2758 [inlined]
ijl_apply_generic at /cache/build/default-amdci4-0/julialang/julia-release-1-dot-9/src/gf.c:2940
_include at ./loading.jl:1924
include at ./Base.jl:457
jfptr_include_43521.clone_1 at /home/karim/.julia/juliaup/julia-1.9.0+0.x64.linux.gnu/lib/julia/sys.so (unknown line)
_jl_invoke at /cache/build/default-amdci4-0/julialang/julia-release-1-dot-9/src/gf.c:2758 [inlined]
ijl_apply_generic at /cache/build/default-amdci4-0/julialang/julia-release-1-dot-9/src/gf.c:2940
jl_apply at /cache/build/default-amdci4-0/julialang/julia-release-1-dot-9/src/julia.h:1879 [inlined]
do_call at /cache/build/default-amdci4-0/julialang/julia-release-1-dot-9/src/interpreter.c:126
eval_value at /cache/build/default-amdci4-0/julialang/julia-release-1-dot-9/src/interpreter.c:226
eval_stmt_value at /cache/build/default-amdci4-0/julialang/julia-release-1-dot-9/src/interpreter.c:177 [inlined]
eval_body at /cache/build/default-amdci4-0/julialang/julia-release-1-dot-9/src/interpreter.c:624
jl_interpret_toplevel_thunk at /cache/build/default-amdci4-0/julialang/julia-release-1-dot-9/src/interpreter.c:762
jl_toplevel_eval_flex at /cache/build/default-amdci4-0/julialang/julia-release-1-dot-9/src/toplevel.c:912
jl_toplevel_eval_flex at /cache/build/default-amdci4-0/julialang/julia-release-1-dot-9/src/toplevel.c:856
jl_toplevel_eval_flex at /cache/build/default-amdci4-0/julialang/julia-release-1-dot-9/src/toplevel.c:856
ijl_toplevel_eval_in at /cache/build/default-amdci4-0/julialang/julia-release-1-dot-9/src/toplevel.c:971
ijl_eval_string at /cache/build/default-amdci4-0/julialang/julia-release-1-dot-9/src/jlapi.c:113
juliacall_cmd at /media/karim/Code-Drive/karimn-code/rtemp/RtmpmfiP37/R.INSTALLc20c91992bc42/JuliaCall/src/JuliaCall.cpp:54
_JuliaCall_juliacall_cmd at /media/karim/Code-Drive/karimn-code/rtemp/RtmpmfiP37/R.INSTALLc20c91992bc42/JuliaCall/src/RcppExports.cpp:33
R_doDotCall at /home/karim/R-builds/R-4.3.0/src/main/dotcode.c:868
do_dotcall at /home/karim/R-builds/R-4.3.0/src/main/dotcode.c:1551
bcEval at /home/karim/R-builds/R-4.3.0/src/main/eval.c:7446
Rf_eval at /home/karim/R-builds/R-4.3.0/src/main/eval.c:1013
R_execClosure at /home/karim/R-builds/R-4.3.0/src/main/eval.c:2187
Rf_applyClosure at /home/karim/R-builds/R-4.3.0/src/main/eval.c:2113
bcEval at /home/karim/R-builds/R-4.3.0/src/main/eval.c:7414
Rf_eval at /home/karim/R-builds/R-4.3.0/src/main/eval.c:1013
R_execClosure at /home/karim/R-builds/R-4.3.0/src/main/eval.c:2187
Rf_applyClosure at /home/karim/R-builds/R-4.3.0/src/main/eval.c:2113
bcEval at /home/karim/R-builds/R-4.3.0/src/main/eval.c:7414
Rf_eval at /home/karim/R-builds/R-4.3.0/src/main/eval.c:1013
R_execClosure at /home/karim/R-builds/R-4.3.0/src/main/eval.c:2187
Rf_applyClosure at /home/karim/R-builds/R-4.3.0/src/main/eval.c:2113
bcEval at /home/karim/R-builds/R-4.3.0/src/main/eval.c:7414
Rf_eval at /home/karim/R-builds/R-4.3.0/src/main/eval.c:1013
R_execClosure at /home/karim/R-builds/R-4.3.0/src/main/eval.c:2187
Rf_applyClosure at /home/karim/R-builds/R-4.3.0/src/main/eval.c:2113
bcEval at /home/karim/R-builds/R-4.3.0/src/main/eval.c:7414
Rf_eval at /home/karim/R-builds/R-4.3.0/src/main/eval.c:1013
R_execClosure at /home/karim/R-builds/R-4.3.0/src/main/eval.c:2187
Rf_applyClosure at /home/karim/R-builds/R-4.3.0/src/main/eval.c:2113
Rf_eval at /home/karim/R-builds/R-4.3.0/src/main/eval.c:1140
Rf_ReplIteration at /home/karim/R-builds/R-4.3.0/src/main/main.c:262
R_ReplConsole at /home/karim/R-builds/R-4.3.0/src/main/main.c:314
run_Rmainloop at /home/karim/R-builds/R-4.3.0/src/main/main.c:1200
main at /home/karim/R-builds/R-4.3.0/src/main/Rmain.c:29
unknown function (ip: 0x7f3f0c829d8f)
__libc_start_main at /usr/lib/x86_64-linux-gnu/libc.so.6 (unknown line)
_start at /opt/R/4.3.0/lib/R/bin/exec/R (unknown line)
Allocations: 1360045 (Pool: 1359338; Big: 707); GC: 2
Segmentation fault (core dumped)
@JackDunnNZ
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The lines at the very top of the trace seem to indicate that Julia is calling back into your R 4.2 install rather than 4.3 during the __init__ of RCall.jl

GetNewPage at /home/karim/R-builds/R-4.2.0/src/main/memory.c:993
Rf_allocVector3 at /home/karim/R-builds/R-4.2.0/src/main/memory.c:2665
Rf_ScalarInteger at /home/karim/R-builds/R-4.2.0/src/main/../../src/include/Rinlinedfuns.h:1002
__init__ at /home/karim/.julia/packages/RCall/LWzAQ/src/setup.jl:189

My guess is that RCall needs to be rebuilt to point to 4.3, maybe try running julia_setup(rebuild=TRUE) and see if that works?

@karimn
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karimn commented May 15, 2023

Still getting a segfault. I tried rebuilding R first but it didn't make any difference.

> JuliaCall::julia_setup(rebuild=TRUE)
Julia version 1.9.0 at location /home/karim/.julia/juliaup/julia-1.9.0+0.x64.linux.gnu/bin will be used.
Loading setup script for JuliaCall...

[19748] signal (11.1): Segmentation fault
in expression starting at /home/karim/R/x86_64-pc-linux-gnu-library/4.3/JuliaCall/julia/setup.jl:80
GetNewPage at /home/karim/R-builds/R-4.2.0/src/main/memory.c:993
Rf_allocVector3 at /home/karim/R-builds/R-4.2.0/src/main/memory.c:2665
Rf_ScalarInteger at /home/karim/R-builds/R-4.2.0/src/main/../../src/include/Rinlinedfuns.h:1002
__init__ at /home/karim/.julia/packages/RCall/LWzAQ/src/setup.jl:189
jfptr___init___371 at /home/karim/.julia/compiled/v1.9/RCall/8GFyb_YlBTL.so (unknown line)
_jl_invoke at /cache/build/default-amdci4-0/julialang/julia-release-1-dot-9/src/gf.c:2758 [inlined]
ijl_apply_generic at /cache/build/default-amdci4-0/julialang/julia-release-1-dot-9/src/gf.c:2940
jl_apply at /cache/build/default-amdci4-0/julialang/julia-release-1-dot-9/src/julia.h:1879 [inlined]
jl_module_run_initializer at /cache/build/default-amdci4-0/julialang/julia-release-1-dot-9/src/toplevel.c:75
ijl_init_restored_modules at /cache/build/default-amdci4-0/julialang/julia-release-1-dot-9/src/module.c:982
register_restored_modules at ./loading.jl:1074
_include_from_serialized at ./loading.jl:1020
_require_search_from_serialized at ./loading.jl:1471
_require at ./loading.jl:1748
_require_prelocked at ./loading.jl:1625
macro expansion at ./loading.jl:1613 [inlined]
macro expansion at ./lock.jl:267 [inlined]
require at ./loading.jl:1576
jfptr_require_38136.clone_1 at /home/karim/.julia/juliaup/julia-1.9.0+0.x64.linux.gnu/lib/julia/sys.so (unknown line)
_jl_invoke at /cache/build/default-amdci4-0/julialang/julia-release-1-dot-9/src/gf.c:2758 [inlined]
ijl_apply_generic at /cache/build/default-amdci4-0/julialang/julia-release-1-dot-9/src/gf.c:2940
jl_apply at /cache/build/default-amdci4-0/julialang/julia-release-1-dot-9/src/julia.h:1879 [inlined]
call_require at /cache/build/default-amdci4-0/julialang/julia-release-1-dot-9/src/toplevel.c:466 [inlined]
eval_import_path at /cache/build/default-amdci4-0/julialang/julia-release-1-dot-9/src/toplevel.c:503
jl_toplevel_eval_flex at /cache/build/default-amdci4-0/julialang/julia-release-1-dot-9/src/toplevel.c:731
jl_eval_module_expr at /cache/build/default-amdci4-0/julialang/julia-release-1-dot-9/src/toplevel.c:203 [inlined]
jl_toplevel_eval_flex at /cache/build/default-amdci4-0/julialang/julia-release-1-dot-9/src/toplevel.c:715
jl_toplevel_eval_flex at /cache/build/default-amdci4-0/julialang/julia-release-1-dot-9/src/toplevel.c:856
ijl_toplevel_eval_in at /cache/build/default-amdci4-0/julialang/julia-release-1-dot-9/src/toplevel.c:971
eval at ./boot.jl:370 [inlined]
include_string at ./loading.jl:1864
_jl_invoke at /cache/build/default-amdci4-0/julialang/julia-release-1-dot-9/src/gf.c:2758 [inlined]
ijl_apply_generic at /cache/build/default-amdci4-0/julialang/julia-release-1-dot-9/src/gf.c:2940
_include at ./loading.jl:1924
include at ./Base.jl:457
jfptr_include_43521.clone_1 at /home/karim/.julia/juliaup/julia-1.9.0+0.x64.linux.gnu/lib/julia/sys.so (unknown line)
_jl_invoke at /cache/build/default-amdci4-0/julialang/julia-release-1-dot-9/src/gf.c:2758 [inlined]
ijl_apply_generic at /cache/build/default-amdci4-0/julialang/julia-release-1-dot-9/src/gf.c:2940
jl_apply at /cache/build/default-amdci4-0/julialang/julia-release-1-dot-9/src/julia.h:1879 [inlined]
do_call at /cache/build/default-amdci4-0/julialang/julia-release-1-dot-9/src/interpreter.c:126
eval_value at /cache/build/default-amdci4-0/julialang/julia-release-1-dot-9/src/interpreter.c:226
eval_stmt_value at /cache/build/default-amdci4-0/julialang/julia-release-1-dot-9/src/interpreter.c:177 [inlined]
eval_body at /cache/build/default-amdci4-0/julialang/julia-release-1-dot-9/src/interpreter.c:624
jl_interpret_toplevel_thunk at /cache/build/default-amdci4-0/julialang/julia-release-1-dot-9/src/interpreter.c:762
jl_toplevel_eval_flex at /cache/build/default-amdci4-0/julialang/julia-release-1-dot-9/src/toplevel.c:912
jl_toplevel_eval_flex at /cache/build/default-amdci4-0/julialang/julia-release-1-dot-9/src/toplevel.c:856
jl_toplevel_eval_flex at /cache/build/default-amdci4-0/julialang/julia-release-1-dot-9/src/toplevel.c:856
ijl_toplevel_eval_in at /cache/build/default-amdci4-0/julialang/julia-release-1-dot-9/src/toplevel.c:971
ijl_eval_string at /cache/build/default-amdci4-0/julialang/julia-release-1-dot-9/src/jlapi.c:113
juliacall_cmd at /media/karim/Code-Drive/karimn-code/rtemp/RtmpJpR1yK/R.INSTALL4c38655b0cde/JuliaCall/src/JuliaCall.cpp:54
_JuliaCall_juliacall_cmd at /media/karim/Code-Drive/karimn-code/rtemp/RtmpJpR1yK/R.INSTALL4c38655b0cde/JuliaCall/src/RcppExports.cpp:33
R_doDotCall at /home/karim/R-builds/R-4.3.0/src/main/dotcode.c:868
do_dotcall at /home/karim/R-builds/R-4.3.0/src/main/dotcode.c:1551
bcEval at /home/karim/R-builds/R-4.3.0/src/main/eval.c:7446
Rf_eval at /home/karim/R-builds/R-4.3.0/src/main/eval.c:1013
R_execClosure at /home/karim/R-builds/R-4.3.0/src/main/eval.c:2187
Rf_applyClosure at /home/karim/R-builds/R-4.3.0/src/main/eval.c:2113
bcEval at /home/karim/R-builds/R-4.3.0/src/main/eval.c:7414
Rf_eval at /home/karim/R-builds/R-4.3.0/src/main/eval.c:1013
R_execClosure at /home/karim/R-builds/R-4.3.0/src/main/eval.c:2187
Rf_applyClosure at /home/karim/R-builds/R-4.3.0/src/main/eval.c:2113
bcEval at /home/karim/R-builds/R-4.3.0/src/main/eval.c:7414
Rf_eval at /home/karim/R-builds/R-4.3.0/src/main/eval.c:1013
R_execClosure at /home/karim/R-builds/R-4.3.0/src/main/eval.c:2187
Rf_applyClosure at /home/karim/R-builds/R-4.3.0/src/main/eval.c:2113
Rf_eval at /home/karim/R-builds/R-4.3.0/src/main/eval.c:1140
Rf_ReplIteration at /home/karim/R-builds/R-4.3.0/src/main/main.c:262
R_ReplConsole at /home/karim/R-builds/R-4.3.0/src/main/main.c:314
run_Rmainloop at /home/karim/R-builds/R-4.3.0/src/main/main.c:1200
main at /home/karim/R-builds/R-4.3.0/src/main/Rmain.c:29
unknown function (ip: 0x7fb53ea29d8f)
__libc_start_main at /usr/lib/x86_64-linux-gnu/libc.so.6 (unknown line)
_start at /opt/R/4.3.0/lib/R/bin/exec/R (unknown line)
Allocations: 1357865 (Pool: 1357144; Big: 721); GC: 1
Segmentation fault (core dumped)

@JackDunnNZ
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Looks like the same issue as here FWIW: JuliaLang/julia#49864

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@karimn @JackDunnNZ