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Expected Behavior
Being Compiled to system image
Current Behavior
Compile failed
Possible Solution / Implementation
From the error report, it seems like something wrong in the file .julia/packages/BioSequences/7i86L/test/kmers/shuffle.jl
Steps to Reproduce (for bugs)
using PackageCompile
compile_package("BioAlignments")
Context
I try to accelerate the julia startup by compiling the used packages into system image, all other packages went well except then BioAlignment, the error report is listed below:
Updating registry at `~/.julia/registries/General`
Updating git-repo `https://github.com/JuliaRegistries/General.git`
�[?25l�[2K�[?25h Resolving package versions...
Updating `~/.julia/dev/PackageCompiler/packages/BioSequences/Project.toml`
[67c07d97] + Automa v0.8.0
[37cfa864] + BioCore v2.0.5
[3c28c6f8] + BioSymbols v3.1.0
[e1450e63] + BufferedStreams v1.0.0
[861a8166] + Combinatorics v0.7.0
[1cb3b9ac] + IndexableBitVectors v1.0.0
[524e6230] + IntervalTrees v1.0.0
[7200193e] + Twiddle v1.1.0
[37e2e46d] + LinearAlgebra
[de0858da] + Printf
[9a3f8284] + Random
Updating `~/.julia/dev/PackageCompiler/packages/BioSequences/Manifest.toml`
[67c07d97] + Automa v0.8.0
[37cfa864] + BioCore v2.0.5
[3c28c6f8] + BioSymbols v3.1.0
[e1450e63] + BufferedStreams v1.0.0
[19ecbf4d] + Codecs v0.5.0
[861a8166] + Combinatorics v0.7.0
[34da2185] + Compat v2.1.0
[864edb3b] + DataStructures v0.15.0
[1cb3b9ac] + IndexableBitVectors v1.0.0
[524e6230] + IntervalTrees v1.0.0
[bac558e1] + OrderedCollections v1.1.0
[f27b6e38] + Polynomials v0.5.2
[3bb67fe8] + TranscodingStreams v0.9.4
[7200193e] + Twiddle v1.1.0
[ddb6d928] + YAML v0.3.2
[2a0f44e3] + Base64
[ade2ca70] + Dates
[8bb1440f] + DelimitedFiles
[8ba89e20] + Distributed
[b77e0a4c] + InteractiveUtils
[76f85450] + LibGit2
[8f399da3] + Libdl
[37e2e46d] + LinearAlgebra
[56ddb016] + Logging
[d6f4376e] + Markdown
[a63ad114] + Mmap
[44cfe95a] + Pkg
[de0858da] + Printf
[9abbd945] + Profile
[3fa0cd96] + REPL
[9a3f8284] + Random
[ea8e919c] + SHA
[9e88b42a] + Serialization
[1a1011a3] + SharedArrays
[6462fe0b] + Sockets
[2f01184e] + SparseArrays
[10745b16] + Statistics
[8dfed614] + Test
[cf7118a7] + UUIDs
[4ec0a83e] + Unicode
Resolving package versions...
Updating `~/.julia/dev/PackageCompiler/packages/BioSequences/Project.toml`
[9b87118b] + PackageCompiler v0.6.3
[44cfe95a] + Pkg
Updating `~/.julia/dev/PackageCompiler/packages/BioSequences/Manifest.toml`
[c7e460c6] + ArgParse v0.6.2
[9e28174c] + BinDeps v0.8.10
[b99e7846] + BinaryProvider v0.5.4
[0862f596] + HTTPClient v0.2.1
[b27032c2] + LibCURL v0.5.0
[522f3ed2] + LibExpat v0.5.0
[2ec943e9] + Libz v1.0.0
[9b87118b] + PackageCompiler v0.6.3
[b718987f] + TextWrap v0.3.0
[30578b45] + URIParser v0.4.0
[c17dfb99] + WinRPM v0.4.2
signal (11): Segmentation fault
in expression starting at /home/chensy/.julia/packages/BioSequences/7i86L/test/kmers/shuffle.jl:1
jl_static_show_x_ at /buildworker/worker/package_linux64/build/src/rtutils.c:657
jl_static_show_x at /buildworker/worker/package_linux64/build/src/rtutils.c:1030 [inlined]
jl_static_show_x_ at /buildworker/worker/package_linux64/build/src/rtutils.c:702
jl_static_show_x at /buildworker/worker/package_linux64/build/src/rtutils.c:1030 [inlined]
jl_static_show at /buildworker/worker/package_linux64/build/src/rtutils.c:1035
jl_mt_assoc_by_type at /buildworker/worker/package_linux64/build/src/gf.c:1130
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2187
do_call at /buildworker/worker/package_linux64/build/src/interpreter.c:323
eval_value at /buildworker/worker/package_linux64/build/src/interpreter.c:411
eval_stmt_value at /buildworker/worker/package_linux64/build/src/interpreter.c:362 [inlined]
eval_body at /buildworker/worker/package_linux64/build/src/interpreter.c:773
eval_body at /buildworker/worker/package_linux64/build/src/interpreter.c:689
eval_body at /buildworker/worker/package_linux64/build/src/interpreter.c:689
eval_body at /buildworker/worker/package_linux64/build/src/interpreter.c:689
jl_interpret_toplevel_thunk_callback at /buildworker/worker/package_linux64/build/src/interpreter.c:885
unknown function(ip: 0xfffffffffffffffe)
unknown function(ip: 0x7ff0a474e2bf)
unknown function(ip: 0x66)
jl_interpret_toplevel_thunk at /buildworker/worker/package_linux64/build/src/interpreter.c:894
jl_toplevel_eval_flex at /buildworker/worker/package_linux64/build/src/toplevel.c:764
jl_parse_eval_all at /buildworker/worker/package_linux64/build/src/ast.c:883
jl_load at /buildworker/worker/package_linux64/build/src/toplevel.c:826
include at ./boot.jl:326 [inlined]
include_relative at ./loading.jl:1038
include at ./sysimg.jl:29 [inlined]
include at /home/chensy/.julia/packages/BioSequences/7i86L/test/runtests.jl:1
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2219
do_call at /buildworker/worker/package_linux64/build/src/interpreter.c:323
eval_value at /buildworker/worker/package_linux64/build/src/interpreter.c:411
eval_stmt_value at /buildworker/worker/package_linux64/build/src/interpreter.c:362 [inlined]
eval_body at /buildworker/worker/package_linux64/build/src/interpreter.c:773
eval_body at /buildworker/worker/package_linux64/build/src/interpreter.c:689
eval_body at /buildworker/worker/package_linux64/build/src/interpreter.c:689
jl_interpret_toplevel_thunk_callback at /buildworker/worker/package_linux64/build/src/interpreter.c:885
unknown function(ip: 0xfffffffffffffffe)
unknown function(ip: 0x7ff0cbab617f)
unknown function(ip: 0x33)
jl_interpret_toplevel_thunk at /buildworker/worker/package_linux64/build/src/interpreter.c:894
jl_toplevel_eval_flex at /buildworker/worker/package_linux64/build/src/toplevel.c:764
jl_eval_module_expr at /buildworker/worker/package_linux64/build/src/toplevel.c:179
jl_toplevel_eval_flex at /buildworker/worker/package_linux64/build/src/toplevel.c:614
jl_parse_eval_all at /buildworker/worker/package_linux64/build/src/ast.c:883
jl_load at /buildworker/worker/package_linux64/build/src/toplevel.c:826
include at ./boot.jl:326 [inlined]
include_relative at ./loading.jl:1038
include at ./sysimg.jl:29
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2219
include at ./client.jl:403
jl_fptr_trampoline at /buildworker/worker/package_linux64/build/src/gf.c:1864
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2219
do_call at /buildworker/worker/package_linux64/build/src/interpreter.c:323
eval_value at /buildworker/worker/package_linux64/build/src/interpreter.c:411
eval_stmt_value at /buildworker/worker/package_linux64/build/src/interpreter.c:362 [inlined]
eval_body at /buildworker/worker/package_linux64/build/src/interpreter.c:773
eval_body at /buildworker/worker/package_linux64/build/src/interpreter.c:689
jl_interpret_toplevel_thunk_callback at /buildworker/worker/package_linux64/build/src/interpreter.c:885
unknown function(ip: 0xfffffffffffffffe)
unknown function(ip: 0x7ff0cb28a49f)
unknown function(ip: (nil))
jl_interpret_toplevel_thunk at /buildworker/worker/package_linux64/build/src/interpreter.c:894
jl_toplevel_eval_flex at /buildworker/worker/package_linux64/build/src/toplevel.c:764
jl_parse_eval_all at /buildworker/worker/package_linux64/build/src/ast.c:883
jl_load at /buildworker/worker/package_linux64/build/src/toplevel.c:826
include at ./boot.jl:326 [inlined]
include_relative at ./loading.jl:1038
include at ./sysimg.jl:29
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2219
exec_options at ./client.jl:267
_start at ./client.jl:436
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2219
jl_apply at /buildworker/worker/package_linux64/build/ui/../src/julia.h:1571 [inlined]
true_main at /buildworker/worker/package_linux64/build/ui/repl.c:96
main at /buildworker/worker/package_linux64/build/ui/repl.c:217
__libc_start_main at /build/eglibc-ripdx6/eglibc-2.19/csu/libc-start.c:287
_start at /home/chensy/julia-1.1.0/bin/julia (unknown line)
Allocations: 140966623 (Pool: 140931781; Big: 34842); GC: 278
[ Info: Registered package BioSequences, using already given UUID: 7e6ae17a-c86d-528c-b3b9-7f778a29fe59
ERROR: LoadError: failed process: Process(`/home/chensy/julia-1.1.0/bin/julia --compile=all --optimize=0 -g1 --trace-compile=/home/chensy/.julia/dev/PackageCompiler/packages/precompile_tmp.jl --history-file=yes --code-coverage=none --inline=yes --math-mode=ieee --handle-signals=yes --warn-overwrite=no --compile=yes --depwarn=yes --cpu-target=native --track-allocation=none --sysimage-native-code=yes --sysimage=/home/chensy/julia-1.1.0/lib/julia/sys.so -g1 --compiled-modules=yes --optimize=2 /home/chensy/.julia/dev/PackageCompiler/sysimg/run_julia_code.jl`, ProcessSignaled(11)) [0]
Stacktrace:
[1] error(::String, ::Base.Process, ::String, ::Int64, ::String) at ./error.jl:42
[2] pipeline_error at ./process.jl:785 [inlined]
[3] #run#515(::Bool, ::Function, ::Cmd) at ./process.jl:726
[4] #run_julia#1 at ./process.jl:724 [inlined]
[5] (::getfield(PackageCompiler, Symbol("#kw##run_julia")))(::NamedTuple{(:compile, :O, :g, :trace_compile),Tuple{String,Int64,Int64,String}}, ::typeof(PackageCompiler.run_julia), ::String) at ./none:0
[6] snoop(::Symbol, ::String, ::String, ::String, ::Bool, ::Array{Any,1}) at /home/chensy/.julia/dev/PackageCompiler/src/snooping.jl:34
[7] (::getfield(PackageCompiler, Symbol("##35#37")){Array{Any,1},Tuple{Symbol},Dict{Any,Any},String,Dict{String,Array{Dict{String,Any},1}}})(::IOStream) at /home/chensy/.julia/dev/PackageCompiler/src/snooping.jl:124
[8] #open#310(::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}, ::Function, ::getfield(PackageCompiler, Symbol("##35#37")){Array{Any,1},Tuple{Symbol},Dict{Any,Any},String,Dict{String,Array{Dict{String,Any},1}}}, ::String, ::Vararg{String,N} where N) at ./iostream.jl:369
[9] open at ./iostream.jl:367 [inlined]
[10] #snoop_packages#34 at /home/chensy/.julia/dev/PackageCompiler/src/snooping.jl:110 [inlined]
[11] #snoop_packages at ./none:0 [inlined]
[12] #compile_package#67(::Bool, ::Bool, ::Bool, ::Nothing, ::Bool, ::Function, ::Tuple{String,String}) at /home/chensy/.julia/dev/PackageCompiler/src/PackageCompiler.jl:122
[13] #compile_package#64 at /home/chensy/.julia/dev/PackageCompiler/src/PackageCompiler.jl:116 [inlined]
[14] compile_package(::String) at /home/chensy/.julia/dev/PackageCompiler/src/PackageCompiler.jl:88
[15] top-level scope at none:0
[16] include at ./boot.jl:326 [inlined]
[17] include_relative(::Module, ::String) at ./loading.jl:1038
[18] include(::Module, ::String) at ./sysimg.jl:29
[19] exec_options(::Base.JLOptions) at ./client.jl:267
[20] _start() at ./client.jl:436
in expression starting at /home/chensy/jatt/generate_log.jl:2
Your Environment
Package Version used: BioAlignments 1.0.0
Julia Version used: 1.1.0
Operating System and version (desktop or mobile): Ubuntu 16.04
Link to your project:
The text was updated successfully, but these errors were encountered:
Expected Behavior
Being Compiled to system image
Current Behavior
Compile failed
Possible Solution / Implementation
From the error report, it seems like something wrong in the file .julia/packages/BioSequences/7i86L/test/kmers/shuffle.jl
Steps to Reproduce (for bugs)
Context
I try to accelerate the julia startup by compiling the used packages into system image, all other packages went well except then BioAlignment, the error report is listed below:
Your Environment
The text was updated successfully, but these errors were encountered: