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Can't compiled by PackageCompile #30

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aqzas opened this issue May 28, 2019 · 0 comments
Open

Can't compiled by PackageCompile #30

aqzas opened this issue May 28, 2019 · 0 comments

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@aqzas
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aqzas commented May 28, 2019

This template is rather extensive. Fill out all that you can, if are a new contributor or you're unsure about any section, leave it unchanged and a reviewer will help you 😄. This template is simply a tool to help everyone remember the BioJulia guidelines, if you feel anything in this template is not relevant, simply delete it.

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:
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@aqzas