JuliaInterop / JuliaInterop/JuliaCall
Segfault in atexit hook on Julia 1.9
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Description
I am seeing the following segfault when running the following example on Julia 1.9:
$ julia -e 'using RCall; R"JuliaCall::julia_setup()"'
┌ Warning: RCall.jl: Julia version 1.9.0 at location /Users/jack/.julia/juliaup/julia-1.9.0+0.x64.apple.darwin14/bin will be used.
│ Loading setup script for JuliaCall...
└ @ RCall ~/.julia/packages/RCall/LWzAQ/src/io.jl:172
┌ Warning: RCall.jl: Finish loading setup script for JuliaCall.
└ @ RCall ~/.julia/packages/RCall/LWzAQ/src/io.jl:172
[48844] signal (11.1): Segmentation fault: 11
in expression starting at none:0
ijl_eh_restore_state at /Users/jack/.julia/juliaup/julia-1.9.0+0.x64.apple.darwin14/lib/julia/libjulia-internal.1.9.dylib (unknown line)
_atexit at ./initdefs.jl:386
jfptr__atexit_44795.clone_1 at /Users/jack/.julia/juliaup/julia-1.9.0+0.x64.apple.darwin14/lib/julia/sys.dylib (unknown line)
ijl_apply_generic at /Users/jack/.julia/juliaup/julia-1.9.0+0.x64.apple.darwin14/lib/julia/libjulia-internal.1.9.dylib (unknown line)
ijl_atexit_hook at /Users/jack/.julia/juliaup/julia-1.9.0+0.x64.apple.darwin14/lib/julia/libjulia-internal.1.9.dylib (unknown line)
jl_repl_entrypoint at /Users/jack/.julia/juliaup/julia-1.9.0+0.x64.apple.darwin14/lib/julia/libjulia-internal.1.9.dylib (unknown line)
Allocations: 6538113 (Pool: 6531359; Big: 6754); GC: 10
[1] 48843 segmentation fault julia --depwarn=yes -e
If I run on Julia 1.8 or earlier, it works fine.
Based on the atexit in the stacktrace, I tried disabling the atexit hook in JuliaCall here and that made the segfault go away, so presumably there is something in that function that Julia 1.9 does not like. I haven't been able to go any deeper though
Session Info
─ Session info ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
setting value
version R version 4.3.0 (2023-04-21)
os macOS Ventura 13.1
system x86_64, darwin20
ui X11
language (EN)
collate en_NZ.UTF-8
ctype en_NZ.UTF-8
tz America/New_York
date 2023-05-12
pandoc 2.11.3.2 @ /usr/local/bin/pandoc
─ Packages ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
package * version date (UTC) lib source
cachem 1.0.8 2023-05-01 [1] CRAN (R 4.3.0)
callr 3.7.3 2022-11-02 [1] CRAN (R 4.3.0)
cli 3.6.1 2023-03-23 [1] CRAN (R 4.3.0)
crayon 1.5.2 2022-09-29 [1] CRAN (R 4.3.0)
devtools 2.4.5 2022-10-11 [1] CRAN (R 4.3.0)
digest 0.6.31 2022-12-11 [1] CRAN (R 4.3.0)
ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.3.0)
fastmap 1.1.1 2023-02-24 [1] CRAN (R 4.3.0)
fs 1.6.2 2023-04-25 [1] CRAN (R 4.3.0)
glue 1.6.2 2022-02-24 [1] CRAN (R 4.3.0)
htmltools 0.5.5 2023-03-23 [1] CRAN (R 4.3.0)
htmlwidgets 1.6.2 2023-03-17 [1] CRAN (R 4.3.0)
httpuv 1.6.11 2023-05-11 [1] CRAN (R 4.3.0)
later 1.3.1 2023-05-02 [1] CRAN (R 4.3.0)
lifecycle 1.0.3 2022-10-07 [1] CRAN (R 4.3.0)
magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.3.0)
memoise 2.0.1 2021-11-26 [1] CRAN (R 4.3.0)
mime 0.12 2021-09-28 [1] CRAN (R 4.3.0)
miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 4.3.0)
pkgbuild 1.4.0 2022-11-27 [1] CRAN (R 4.3.0)
pkgload 1.3.2 2022-11-16 [1] CRAN (R 4.3.0)
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.3.0)
processx 3.8.1 2023-04-18 [1] CRAN (R 4.3.0)
profvis 0.3.8 2023-05-02 [1] CRAN (R 4.3.0)
promises 1.2.0.1 2021-02-11 [1] CRAN (R 4.3.0)
ps 1.7.5 2023-04-18 [1] CRAN (R 4.3.0)
purrr 1.0.1 2023-01-10 [1] CRAN (R 4.3.0)
R6 2.5.1 2021-08-19 [1] CRAN (R 4.3.0)
Rcpp 1.0.10 2023-01-22 [1] CRAN (R 4.3.0)
remotes 2.4.2 2021-11-30 [1] CRAN (R 4.3.0)
rlang 1.1.1 2023-04-28 [1] CRAN (R 4.3.0)
sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.3.0)
shiny 1.7.4 2022-12-15 [1] CRAN (R 4.3.0)
stringi 1.7.12 2023-01-11 [1] CRAN (R 4.3.0)
stringr 1.5.0 2022-12-02 [1] CRAN (R 4.3.0)
urlchecker 1.0.1 2021-11-30 [1] CRAN (R 4.3.0)
usethis 2.1.6 2022-05-25 [1] CRAN (R 4.3.0)
vctrs 0.6.2 2023-04-19 [1] CRAN (R 4.3.0)
xtable 1.8-4 2019-04-21 [1] CRAN (R 4.3.0)
[1] /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library
───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Reproduce the failure with the JuliaCall example julia -e 'using RCall; R"JuliaCall::julia_setup()"' on Julia 1.9 and compare it with Julia 1.8. Inspect the atexit hook in R/zzz.R at the linked lines, then trace its interaction with the JuliaCall setup. Done means the hook no longer causes a segmentation fault on Julia 1.9.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- julia, r
- Domain
- backend
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100