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Segfault when reading into dataframe with a transpose #1141

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yakir12 opened this issue Sep 2, 2024 · 0 comments
Open

Segfault when reading into dataframe with a transpose #1141

yakir12 opened this issue Sep 2, 2024 · 0 comments

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@yakir12
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yakir12 commented Sep 2, 2024

(Edit: now simplified and removed DataFrames)
The following MWE (file table.csv attached) will segfault:

table.csv

using CSV
file = "table.csv"
df = CSV.File(file; transpose=true) # segfaults

stacktrace:

[317035] signal (11.1): Segmentation fault
in expression starting at REPL[6]:1
getindex at ./essentials.jl:13 [inlined]
peekbyte at /home/yakir/.julia/packages/Parsers/fKIy3/src/utils.jl:339 [inlined]
#9 at /home/yakir/.julia/packages/Parsers/fKIy3/src/components.jl:7 [inlined]
_xparse at /home/yakir/.julia/packages/Parsers/fKIy3/src/Parsers.jl:407
xparse at /home/yakir/.julia/packages/Parsers/fKIy3/src/Parsers.jl:418 [inlined]
xparse at /home/yakir/.julia/packages/Parsers/fKIy3/src/Parsers.jl:412 [inlined]
xparse at /home/yakir/.julia/packages/Parsers/fKIy3/src/Parsers.jl:412 [inlined]
parsevalue! at /home/yakir/.julia/packages/CSV/cwX2w/src/file.jl:776 [inlined]
parserow at /home/yakir/.julia/packages/CSV/cwX2w/src/file.jl:604
promotetostring! at /home/yakir/.julia/packages/CSV/cwX2w/src/file.jl:894
parserow at /home/yakir/.julia/packages/CSV/cwX2w/src/file.jl:668 [inlined]
parsefilechunk! at /home/yakir/.julia/packages/CSV/cwX2w/src/file.jl:550
jfptr_parsefilechunkNOT._6095 at /home/yakir/.julia/compiled/v1.10/CSV/HHBkp_p7t0U.so (unknown line)
_jl_invoke at /cache/build/builder-amdci4-4/julialang/julia-release-1-dot-10/src/gf.c:2895 [inlined]
ijl_apply_generic at /cache/build/builder-amdci4-4/julialang/julia-release-1-dot-10/src/gf.c:3077
File at /home/yakir/.julia/packages/CSV/cwX2w/src/file.jl:290
File at /home/yakir/.julia/packages/CSV/cwX2w/src/file.jl:227 [inlined]
#File#32 at /home/yakir/.julia/packages/CSV/cwX2w/src/file.jl:223 [inlined]
File at /home/yakir/.julia/packages/CSV/cwX2w/src/file.jl:162
unknown function (ip: 0x7fc0a6524e0d)
_jl_invoke at /cache/build/builder-amdci4-4/julialang/julia-release-1-dot-10/src/gf.c:2895 [inlined]
ijl_apply_generic at /cache/build/builder-amdci4-4/julialang/julia-release-1-dot-10/src/gf.c:3077
jl_apply at /cache/build/builder-amdci4-4/julialang/julia-release-1-dot-10/src/julia.h:1982 [inlined]
do_call at /cache/build/builder-amdci4-4/julialang/julia-release-1-dot-10/src/interpreter.c:126
eval_value at /cache/build/builder-amdci4-4/julialang/julia-release-1-dot-10/src/interpreter.c:223
eval_stmt_value at /cache/build/builder-amdci4-4/julialang/julia-release-1-dot-10/src/interpreter.c:174 [inlined]
eval_body at /cache/build/builder-amdci4-4/julialang/julia-release-1-dot-10/src/interpreter.c:617
jl_interpret_toplevel_thunk at /cache/build/builder-amdci4-4/julialang/julia-release-1-dot-10/src/interpreter.c:775
jl_toplevel_eval_flex at /cache/build/builder-amdci4-4/julialang/julia-release-1-dot-10/src/toplevel.c:934
jl_toplevel_eval_flex at /cache/build/builder-amdci4-4/julialang/julia-release-1-dot-10/src/toplevel.c:877
ijl_toplevel_eval_in at /cache/build/builder-amdci4-4/julialang/julia-release-1-dot-10/src/toplevel.c:985
eval at ./boot.jl:385 [inlined]
eval_user_input at /cache/build/builder-amdci4-4/julialang/julia-release-1-dot-10/usr/share/julia/stdlib/v1.10/REPL/src/REPL.jl:150
repl_backend_loop at /cache/build/builder-amdci4-4/julialang/julia-release-1-dot-10/usr/share/julia/stdlib/v1.10/REPL/src/REPL.jl:246
#start_repl_backend#46 at /cache/build/builder-amdci4-4/julialang/julia-release-1-dot-10/usr/share/julia/stdlib/v1.10/REPL/src/REPL.jl:231
start_repl_backend at /cache/build/builder-amdci4-4/julialang/julia-release-1-dot-10/usr/share/julia/stdlib/v1.10/REPL/src/REPL.jl:228
_jl_invoke at /cache/build/builder-amdci4-4/julialang/julia-release-1-dot-10/src/gf.c:2895 [inlined]
ijl_apply_generic at /cache/build/builder-amdci4-4/julialang/julia-release-1-dot-10/src/gf.c:3077
#run_repl#59 at /cache/build/builder-amdci4-4/julialang/julia-release-1-dot-10/usr/share/julia/stdlib/v1.10/REPL/src/REPL.jl:389
run_repl at /cache/build/builder-amdci4-4/julialang/julia-release-1-dot-10/usr/share/julia/stdlib/v1.10/REPL/src/REPL.jl:375
jfptr_run_repl_91805.1 at /home/yakir/.julia/juliaup/julia-1.10.5+0.x64.linux.gnu/lib/julia/sys.so (unknown line)
_jl_invoke at /cache/build/builder-amdci4-4/julialang/julia-release-1-dot-10/src/gf.c:2895 [inlined]
ijl_apply_generic at /cache/build/builder-amdci4-4/julialang/julia-release-1-dot-10/src/gf.c:3077
#1013 at ./client.jl:432
jfptr_YY.1013_82772.1 at /home/yakir/.julia/juliaup/julia-1.10.5+0.x64.linux.gnu/lib/julia/sys.so (unknown line)
_jl_invoke at /cache/build/builder-amdci4-4/julialang/julia-release-1-dot-10/src/gf.c:2895 [inlined]
ijl_apply_generic at /cache/build/builder-amdci4-4/julialang/julia-release-1-dot-10/src/gf.c:3077
jl_apply at /cache/build/builder-amdci4-4/julialang/julia-release-1-dot-10/src/julia.h:1982 [inlined]
jl_f__call_latest at /cache/build/builder-amdci4-4/julialang/julia-release-1-dot-10/src/builtins.c:812
#invokelatest#2 at ./essentials.jl:892 [inlined]
invokelatest at ./essentials.jl:889 [inlined]
run_main_repl at ./client.jl:416
exec_options at ./client.jl:333
_start at ./client.jl:552
jfptr__start_82798.1 at /home/yakir/.julia/juliaup/julia-1.10.5+0.x64.linux.gnu/lib/julia/sys.so (unknown line)
_jl_invoke at /cache/build/builder-amdci4-4/julialang/julia-release-1-dot-10/src/gf.c:2895 [inlined]
ijl_apply_generic at /cache/build/builder-amdci4-4/julialang/julia-release-1-dot-10/src/gf.c:3077
jl_apply at /cache/build/builder-amdci4-4/julialang/julia-release-1-dot-10/src/julia.h:1982 [inlined]
true_main at /cache/build/builder-amdci4-4/julialang/julia-release-1-dot-10/src/jlapi.c:582
jl_repl_entrypoint at /cache/build/builder-amdci4-4/julialang/julia-release-1-dot-10/src/jlapi.c:731
main at /cache/build/builder-amdci4-4/julialang/julia-release-1-dot-10/cli/loader_exe.c:58
unknown function (ip: 0x7fc0bdef1249)
__libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
unknown function (ip: 0x4010b8)
Allocations: 9153978 (Pool: 9147526; Big: 6452); GC: 11
Segmentation fault

Version info:

(jl_Buj5BW) pkg> st
Status `/tmp/jl_Buj5BW/Project.toml`
  [336ed68f] CSV v0.10.14

julia> versioninfo()
Julia Version 1.10.5
Commit 6f3fdf7b362 (2024-08-27 14:19 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
  CPU: 32 × AMD Ryzen Threadripper 2950X 16-Core Processor
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-15.0.7 (ORCJIT, znver1)
Threads: 1 default, 0 interactive, 1 GC (on 32 virtual cores)
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