Segmentation fault (core dumped) - Conda installation

[ctroupin]

How to reproduce

1. Install everything with conda (under Linux):

1. Download from https://conda.io/projects/conda/en/latest/user-guide/install/linux.html
2. Run installation script: bash bash Miniconda3-latest-Linux-x86_64.sh
3. Modify the PATH environment variable: bash export PATH=$PATH:/home/ctroupin/miniconda3/bin
4. Install R, Julia, and the different R modules:

   conda install conda-forge::r-base
   conda install conda-forge::r-juliaup
   ...

   • all the R packages to be installed with conda, for example:

     conda install r::r-ncdf4

2. Run the following commands

Ensure that you use the R installed via conda: bash /home/ctroupin/miniconda3/bin/R

> library(JuliaCall)
> julia_command("using DIVAnd")

Julia version 1.10.2 at location /home/ctroupin/.julia/juliaup/julia-1.10.2+0.x64.linux.gnu/bin will be used.
Loading setup script for JuliaCall...

[79609] signal (11.1): Segmentation fault
in expression starting at /home/ctroupin/miniconda3/lib/R/library/JuliaCall/julia/setup.jl:80
unknown function (ip: 0x7ba471993dd0)
Rf_allocVector3 at /usr/lib/R/lib/libR.so (unknown line)
Rf_ScalarInteger at /usr/lib/R/lib/libR.so (unknown line)
__init__ at /home/ctroupin/.julia/packages/RCall/dDAVd/src/setup.jl:195
jfptr___init___3818 at /home/ctroupin/.julia/compiled/v1.10/RCall/8GFyb_ZvDSa.so (unknown line)
_jl_invoke at /cache/build/builder-amdci5-1/julialang/julia-release-1-dot-10/src/gf.c:2894 [inlined]
ijl_apply_generic at /cache/build/builder-amdci5-1/julialang/julia-release-1-dot-10/src/gf.c:3076
jl_apply at /cache/build/builder-amdci5-1/julialang/julia-release-1-dot-10/src/julia.h:1982 [inlined]
jl_module_run_initializer at /cache/build/builder-amdci5-1/julialang/julia-release-1-dot-10/src/toplevel.c:76
run_module_init at ./loading.jl:1134
register_restored_modules at ./loading.jl:1122
_include_from_serialized at ./loading.jl:1067
_require_search_from_serialized at ./loading.jl:1581
_require at ./loading.jl:1938
__require_prelocked at ./loading.jl:1812
jfptr___require_prelocked_80777.1 at /home/ctroupin/.julia/juliaup/julia-1.10.2+0.x64.linux.gnu/lib/julia/sys.so (unknown line)
_jl_invoke at /cache/build/builder-amdci5-1/julialang/julia-release-1-dot-10/src/gf.c:2894 [inlined]
ijl_apply_generic at /cache/build/builder-amdci5-1/julialang/julia-release-1-dot-10/src/gf.c:3076
jl_apply at /cache/build/builder-amdci5-1/julialang/julia-release-1-dot-10/src/julia.h:1982 [inlined]
jl_f__call_in_world at /cache/build/builder-amdci5-1/julialang/julia-release-1-dot-10/src/builtins.c:831
#invoke_in_world#3 at ./essentials.jl:926 [inlined]
invoke_in_world at ./essentials.jl:923 [inlined]
_require_prelocked at ./loading.jl:1803
macro expansion at ./loading.jl:1790 [inlined]
macro expansion at ./lock.jl:267 [inlined]
__require at ./loading.jl:1753
jfptr___require_80742.1 at /home/ctroupin/.julia/juliaup/julia-1.10.2+0.x64.linux.gnu/lib/julia/sys.so (unknown line)
_jl_invoke at /cache/build/builder-amdci5-1/julialang/julia-release-1-dot-10/src/gf.c:2894 [inlined]
ijl_apply_generic at /cache/build/builder-amdci5-1/julialang/julia-release-1-dot-10/src/gf.c:3076
jl_apply at /cache/build/builder-amdci5-1/julialang/julia-release-1-dot-10/src/julia.h:1982 [inlined]
jl_f__call_in_world at /cache/build/builder-amdci5-1/julialang/julia-release-1-dot-10/src/builtins.c:831
#invoke_in_world#3 at ./essentials.jl:926 [inlined]
invoke_in_world at ./essentials.jl:923 [inlined]
require at ./loading.jl:1746
jfptr_require_80739.1 at /home/ctroupin/.julia/juliaup/julia-1.10.2+0.x64.linux.gnu/lib/julia/sys.so (unknown line)
_jl_invoke at /cache/build/builder-amdci5-1/julialang/julia-release-1-dot-10/src/gf.c:2894 [inlined]
ijl_apply_generic at /cache/build/builder-amdci5-1/julialang/julia-release-1-dot-10/src/gf.c:3076
jl_apply at /cache/build/builder-amdci5-1/julialang/julia-release-1-dot-10/src/julia.h:1982 [inlined]
call_require at /cache/build/builder-amdci5-1/julialang/julia-release-1-dot-10/src/toplevel.c:481 [inlined]
eval_import_path at /cache/build/builder-amdci5-1/julialang/julia-release-1-dot-10/src/toplevel.c:518
jl_toplevel_eval_flex at /cache/build/builder-amdci5-1/julialang/julia-release-1-dot-10/src/toplevel.c:752
jl_eval_module_expr at /cache/build/builder-amdci5-1/julialang/julia-release-1-dot-10/src/toplevel.c:215 [inlined]
jl_toplevel_eval_flex at /cache/build/builder-amdci5-1/julialang/julia-release-1-dot-10/src/toplevel.c:736
jl_toplevel_eval_flex at /cache/build/builder-amdci5-1/julialang/julia-release-1-dot-10/src/toplevel.c:877
ijl_toplevel_eval_in at /cache/build/builder-amdci5-1/julialang/julia-release-1-dot-10/src/toplevel.c:985
eval at ./boot.jl:385 [inlined]
include_string at ./loading.jl:2076
_jl_invoke at /cache/build/builder-amdci5-1/julialang/julia-release-1-dot-10/src/gf.c:2894 [inlined]
ijl_apply_generic at /cache/build/builder-amdci5-1/julialang/julia-release-1-dot-10/src/gf.c:3076
_include at ./loading.jl:2136
include at ./Base.jl:495
jfptr_include_46403.1 at /home/ctroupin/.julia/juliaup/julia-1.10.2+0.x64.linux.gnu/lib/julia/sys.so (unknown line)
_jl_invoke at /cache/build/builder-amdci5-1/julialang/julia-release-1-dot-10/src/gf.c:2894 [inlined]
ijl_apply_generic at /cache/build/builder-amdci5-1/julialang/julia-release-1-dot-10/src/gf.c:3076
jl_apply at /cache/build/builder-amdci5-1/julialang/julia-release-1-dot-10/src/julia.h:1982 [inlined]
do_call at /cache/build/builder-amdci5-1/julialang/julia-release-1-dot-10/src/interpreter.c:126
eval_value at /cache/build/builder-amdci5-1/julialang/julia-release-1-dot-10/src/interpreter.c:223
eval_stmt_value at /cache/build/builder-amdci5-1/julialang/julia-release-1-dot-10/src/interpreter.c:174 [inlined]
eval_body at /cache/build/builder-amdci5-1/julialang/julia-release-1-dot-10/src/interpreter.c:617
jl_interpret_toplevel_thunk at /cache/build/builder-amdci5-1/julialang/julia-release-1-dot-10/src/interpreter.c:775
jl_toplevel_eval_flex at /cache/build/builder-amdci5-1/julialang/julia-release-1-dot-10/src/toplevel.c:934
jl_toplevel_eval_flex at /cache/build/builder-amdci5-1/julialang/julia-release-1-dot-10/src/toplevel.c:877
jl_toplevel_eval_flex at /cache/build/builder-amdci5-1/julialang/julia-release-1-dot-10/src/toplevel.c:877
ijl_toplevel_eval_in at /cache/build/builder-amdci5-1/julialang/julia-release-1-dot-10/src/toplevel.c:985
ijl_eval_string at /cache/build/builder-amdci5-1/julialang/julia-release-1-dot-10/src/jlapi.c:117
_Z13juliacall_cmdPKc at /home/ctroupin/miniconda3/lib/R/library/JuliaCall/libs/JuliaCall.so (unknown line)
_JuliaCall_juliacall_cmd at /home/ctroupin/miniconda3/lib/R/library/JuliaCall/libs/JuliaCall.so (unknown line)
R_doDotCall at /home/ctroupin/miniconda3/lib/R/bin/exec/../../lib/libR.so (unknown line)
do_dotcall at /home/ctroupin/miniconda3/lib/R/bin/exec/../../lib/libR.so (unknown line)
bcEval at /home/ctroupin/miniconda3/lib/R/bin/exec/../../lib/libR.so (unknown line)
Rf_eval at /home/ctroupin/miniconda3/lib/R/bin/exec/../../lib/libR.so (unknown line)
R_execClosure at /home/ctroupin/miniconda3/lib/R/bin/exec/../../lib/libR.so (unknown line)
Rf_applyClosure at /home/ctroupin/miniconda3/lib/R/bin/exec/../../lib/libR.so (unknown line)
bcEval at /home/ctroupin/miniconda3/lib/R/bin/exec/../../lib/libR.so (unknown line)
Rf_eval at /home/ctroupin/miniconda3/lib/R/bin/exec/../../lib/libR.so (unknown line)
R_execClosure at /home/ctroupin/miniconda3/lib/R/bin/exec/../../lib/libR.so (unknown line)
Rf_applyClosure at /home/ctroupin/miniconda3/lib/R/bin/exec/../../lib/libR.so (unknown line)
bcEval at /home/ctroupin/miniconda3/lib/R/bin/exec/../../lib/libR.so (unknown line)
Rf_eval at /home/ctroupin/miniconda3/lib/R/bin/exec/../../lib/libR.so (unknown line)
R_execClosure at /home/ctroupin/miniconda3/lib/R/bin/exec/../../lib/libR.so (unknown line)
Rf_applyClosure at /home/ctroupin/miniconda3/lib/R/bin/exec/../../lib/libR.so (unknown line)
bcEval at /home/ctroupin/miniconda3/lib/R/bin/exec/../../lib/libR.so (unknown line)
Rf_eval at /home/ctroupin/miniconda3/lib/R/bin/exec/../../lib/libR.so (unknown line)
R_execClosure at /home/ctroupin/miniconda3/lib/R/bin/exec/../../lib/libR.so (unknown line)
Rf_applyClosure at /home/ctroupin/miniconda3/lib/R/bin/exec/../../lib/libR.so (unknown line)
bcEval at /home/ctroupin/miniconda3/lib/R/bin/exec/../../lib/libR.so (unknown line)
Rf_eval at /home/ctroupin/miniconda3/lib/R/bin/exec/../../lib/libR.so (unknown line)
R_execClosure at /home/ctroupin/miniconda3/lib/R/bin/exec/../../lib/libR.so (unknown line)
Rf_applyClosure at /home/ctroupin/miniconda3/lib/R/bin/exec/../../lib/libR.so (unknown line)
bcEval at /home/ctroupin/miniconda3/lib/R/bin/exec/../../lib/libR.so (unknown line)
Rf_eval at /home/ctroupin/miniconda3/lib/R/bin/exec/../../lib/libR.so (unknown line)
R_execClosure at /home/ctroupin/miniconda3/lib/R/bin/exec/../../lib/libR.so (unknown line)
Rf_applyClosure at /home/ctroupin/miniconda3/lib/R/bin/exec/../../lib/libR.so (unknown line)
Rf_eval at /home/ctroupin/miniconda3/lib/R/bin/exec/../../lib/libR.so (unknown line)
Rf_ReplIteration at /home/ctroupin/miniconda3/lib/R/bin/exec/../../lib/libR.so (unknown line)
R_ReplConsole at /home/ctroupin/miniconda3/lib/R/bin/exec/../../lib/libR.so (unknown line)
run_Rmainloop at /home/ctroupin/miniconda3/lib/R/bin/exec/../../lib/libR.so (unknown line)
main at /home/ctroupin/miniconda3/lib/R/bin/exec/R (unknown line)
unknown function (ip: 0x7ba4f1829d8f)
__libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
_start at /home/ctroupin/miniconda3/lib/R/bin/exec/R (unknown line)
Allocations: 2907 (Pool: 2899; Big: 8); GC: 0
Segmentation fault (core dumped)