Failed to compile PyPlot

[bliang26]

I was trying to compile PyPlot with

  julia>  compile_package("PyPlot"; force=false, reuse=false)

but got the following error message:

Please submit a bug report with steps to reproduce this fault, and any error messages that follow (in their entirety). Thanks.
Exception: EXCEPTION_ACCESS_VIOLATION at 0x5c4140c5 -- PyUnicode_InternInPlace at C:\Users\bliang26\.julia\conda\3\python36.dll (unknown line)
in expression starting at C:\Users\bliang26\.julia\packages\PackageCompiler\oT98U\sysimg\precompile.jl:18
PyUnicode_InternInPlace at C:\Users\bliang26\.julia\conda\3\python36.dll (unknown line)
PyUnicode_InternFromString at C:\Users\bliang26\.julia\conda\3\python36.dll (unknown line)
PyImport_Import at C:\Users\bliang26\.julia\conda\3\python36.dll (unknown line)
PyImport_ImportModule at C:\Users\bliang26\.julia\conda\3\python36.dll (unknown line)
_pyimport at C:\Users\bliang26\.julia\packages\PyCall\ttONZ\src\PyCall.jl:469
pyimport at C:\Users\bliang26\.julia\packages\PyCall\ttONZ\src\PyCall.jl:493
pyimport_conda at C:\Users\bliang26\.julia\packages\PyCall\ttONZ\src\PyCall.jl:702
jl_fptr_trampoline at /home/Administrator/buildbot/worker/package_win64/build/src\gf.c:1864
jl_apply_generic at /home/Administrator/buildbot/worker/package_win64/build/src\gf.c:2219 [inlined]
jl_apply at /home/Administrator/buildbot/worker/package_win64/build/src\julia.h:1571 [inlined]
jl_invoke at /home/Administrator/buildbot/worker/package_win64/build/src\gf.c:56
pyimport_conda at C:\Users\bliang26\.julia\packages\PyCall\ttONZ\src\PyCall.jl:701 [inlined]
__init__ at C:\Users\bliang26\.julia\packages\PyPlot\cdCMF\src\init.jl:169
jl_fptr_trampoline at /home/Administrator/buildbot/worker/package_win64/build/src\gf.c:1864
jl_apply_generic at /home/Administrator/buildbot/worker/package_win64/build/src\gf.c:2219
top-level scope at C:\Users\bliang26\.julia\packages\PackageCompiler\oT98U\sysimg\precompile.jl:19 [inlined]
top-level scope at .\none:0
jl_fptr_trampoline at /home/Administrator/buildbot/worker/package_win64/build/src\gf.c:1864
jl_toplevel_eval_flex at /home/Administrator/buildbot/worker/package_win64/build/src\toplevel.c:758
jl_parse_eval_all at /home/Administrator/buildbot/worker/package_win64/build/src\ast.c:883
jl_load at /home/Administrator/buildbot/worker/package_win64/build/src\toplevel.c:826 [inlined]
jl_load_ at /home/Administrator/buildbot/worker/package_win64/build/src\toplevel.c:833
include at .\boot.jl:326 [inlined]
include_relative at .\loading.jl:1038
include at .\sysimg.jl:29
jl_apply_generic at /home/Administrator/buildbot/worker/package_win64/build/src\gf.c:2219
do_call at /home/Administrator/buildbot/worker/package_win64/build/src\interpreter.c:323
eval_value at /home/Administrator/buildbot/worker/package_win64/build/src\interpreter.c:411
eval_stmt_value at /home/Administrator/buildbot/worker/package_win64/build/src\interpreter.c:362 [inlined]
eval_body at /home/Administrator/buildbot/worker/package_win64/build/src\interpreter.c:755
jl_interpret_toplevel_thunk_callback at /home/Administrator/buildbot/worker/package_win64/build/src\interpreter.c:885
unknown function (ip: FFFFFFFFFFFFFFFE)
unknown function (ip: 00000000082D339F)
unknown function (ip: 0000000000000000)
jl_toplevel_eval_flex at /home/Administrator/buildbot/worker/package_win64/build/src\toplevel.c:764
jl_toplevel_eval at /home/Administrator/buildbot/worker/package_win64/build/src\toplevel.c:773 [inlined]
jl_toplevel_eval_in at /home/Administrator/buildbot/worker/package_win64/build/src\toplevel.c:793
eval at .\boot.jl:328
jl_fptr_trampoline at /home/Administrator/buildbot/worker/package_win64/build/src\gf.c:1864
jl_apply_generic at /home/Administrator/buildbot/worker/package_win64/build/src\gf.c:2219
do_call at /home/Administrator/buildbot/worker/package_win64/build/src\interpreter.c:323
eval_value at /home/Administrator/buildbot/worker/package_win64/build/src\interpreter.c:411
eval_stmt_value at /home/Administrator/buildbot/worker/package_win64/build/src\interpreter.c:362 [inlined]
eval_body at /home/Administrator/buildbot/worker/package_win64/build/src\interpreter.c:755
jl_interpret_toplevel_thunk_callback at /home/Administrator/buildbot/worker/package_win64/build/src\interpreter.c:885
unknown function (ip: FFFFFFFFFFFFFFFE)
unknown function (ip: 00000000082D316F)
unknown function (ip: 0000000000000002)
jl_toplevel_eval_flex at /home/Administrator/buildbot/worker/package_win64/build/src\toplevel.c:764
jl_parse_eval_all at /home/Administrator/buildbot/worker/package_win64/build/src\ast.c:883
jl_load at /home/Administrator/buildbot/worker/package_win64/build/src\toplevel.c:826 [inlined]
jl_load_ at /home/Administrator/buildbot/worker/package_win64/build/src\toplevel.c:833
include at .\boot.jl:326 [inlined]
include_relative at .\loading.jl:1038
include at .\sysimg.jl:29
jl_fptr_trampoline at /home/Administrator/buildbot/worker/package_win64/build/src\gf.c:1864
jl_apply_generic at /home/Administrator/buildbot/worker/package_win64/build/src\gf.c:2219
exec_options at .\client.jl:267
_start at .\client.jl:436
jl_fptr_trampoline at /home/Administrator/buildbot/worker/package_win64/build/src\gf.c:1864
jl_apply_generic at /home/Administrator/buildbot/worker/package_win64/build/src\gf.c:2219
jl_apply at /home/Administrator/buildbot/worker/package_win64/build/src\julia.h:1571 [inlined]
true_main at /home/Administrator/buildbot/worker/package_win64/build/ui\repl.c:96
wmain at /home/Administrator/buildbot/worker/package_win64/build/ui\repl.c:217
__tmainCRTStartup at /usr/src/debug/mingw64-x86_64-runtime-5.0.3-1/crt\crtexe.c:329
mainCRTStartup at /usr/src/debug/mingw64-x86_64-runtime-5.0.3-1/crt\crtexe.c:212
BaseThreadInitThunk at C:\WINDOWS\System32\KERNEL32.DLL (unknown line)
RtlUserThreadStart at C:\WINDOWS\SYSTEM32\ntdll.dll (unknown line)
Allocations: 8947621 (Pool: 8945343; Big: 2278); GC: 18
ERROR: failed process: Process(`'C:\Users\bliang26\AppData\Local\Julia-1.1.0\bin\julia.exe' '--sysimage=C:\Users\bliang26\.julia\packages\PackageCompiler\oT98U\sysimg\backup\native\sys.dll' --output-o=sys.a --track-allocation=none --code-coverage=none --history-file=yes --inline=yes --math-mode=ieee --compile=yes --track-allocation=none --sysimage-native-code=yes '--sysimage=C:\Users\bliang26\AppData\Local\Julia-1.1.0\lib\julia\sys.dll' --compiled-modules=yes --optimize=2 'C:\Users\bliang26\.julia\packages\PackageCompiler\oT98U\sysimg\run_julia_code.jl'`, ProcessExited(1)) [1]
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 at .\process.jl:724 [inlined]
 [5] #run_julia#1 at C:\Users\bliang26\.julia\packages\PackageCompiler\oT98U\src\compiler_flags.jl:225 [inlined]
 [6] #run_julia at .\none:0 [inlined]
 [7] (::getfield(PackageCompiler, Symbol("##13#14")){Base.Iterators.Pairs{Symbol,Any,NTuple{14,Symbol},NamedTuple{(:sysimage, :startup_file, :handle_signals, :sysimage_native_code, :compiled_modules, :depwarn, :warn_overwrite, :compile, :cpu_target, :optimize, :debug_level, :inline, :check_bounds, :math_mode),Tuple{String,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing}}},String})() at C:\Users\bliang26\.julia\packages\PackageCompiler\oT98U\src\static_julia.jl:262
 [8] cd(::getfield(PackageCompiler, Symbol("##13#14")){Base.Iterators.Pairs{Symbol,Any,NTuple{14,Symbol},NamedTuple{(:sysimage, :startup_file, :handle_signals, :sysimage_native_code, :compiled_modules, :depwarn, :warn_overwrite, :compile, :cpu_target, :optimize, :debug_level, :inline, :check_bounds, :math_mode),Tuple{String,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing}}},String}, ::String) at .\file.jl:85
 [9] #build_object#12(::Base.Iterators.Pairs{Symbol,Any,NTuple{14,Symbol},NamedTuple{(:sysimage, :startup_file, :handle_signals, :sysimage_native_code, :compiled_modules, :depwarn, :warn_overwrite, :compile, :cpu_target, :optimize, :debug_level, :inline, :check_bounds, :math_mode),Tuple{String,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing}}}, ::Function, ::String, ::String, ::String, ::Bool) at C:\Users\bliang26\.julia\packages\PackageCompiler\oT98U\src\static_julia.jl:261
 [10] #build_object at .\none:0 [inlined]
 [11] build_object(::String, ::String, ::String, ::Bool, ::String, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing) at C:\Users\bliang26\.julia\packages\PackageCompiler\oT98U\src\static_julia.jl:240
 [12] #static_julia#5(::Nothing, ::Bool, ::Bool, ::String, ::String, ::Nothing, ::Bool, ::Bool, ::Bool, ::Bool, ::Bool, ::Bool, ::Bool, ::Bool, ::Nothing, ::Bool, ::Bool, ::String, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::typeof(static_julia), ::String) at C:\Users\bliang26\.julia\packages\PackageCompiler\oT98U\src\static_julia.jl:161
 [13] #static_julia at .\none:0 [inlined]
 [14] #build_sysimg#29(::Bool, ::Bool, ::Bool, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::typeof(PackageCompiler.build_sysimg), ::String, ::String) at C:\Users\bliang26\.julia\packages\PackageCompiler\oT98U\src\api.jl:25
 [15] #build_sysimg at .\none:0 [inlined]
 [16] #compile_package#67(::Bool, ::Bool, ::Bool, ::Nothing, ::Bool, ::Function, ::Tuple{String,String}) at C:\Users\bliang26\.julia\packages\PackageCompiler\oT98U\src\PackageCompiler.jl:130
 [17] #compile_package at .\none:0 [inlined]
 [18] #compile_package#64 at C:\Users\bliang26\.julia\packages\PackageCompiler\oT98U\src\PackageCompiler.jl:94 [inlined]
 [19] (::getfield(PackageCompiler, Symbol("#kw##compile_package")))(::NamedTuple{(:force, :reuse),Tuple{Bool,Bool}}, ::typeof(compile_package), ::String) at .\none:0
 [20] top-level scope at none:0

PyCall was set up by the Conda.jl package. And here's my version info:

julia> versioninfo()
Julia Version 1.1.0
Commit 80516ca202 (2019-01-21 21:24 UTC)
Platform Info:
  OS: Windows (x86_64-w64-mingw32)
  CPU: Intel(R) Xeon(R) Gold 5118 CPU @ 2.30GHz
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-6.0.1 (ORCJIT, skylake)

[asinghvi17]

You may want to raise this on www.github.com/JuliaPy/PyCall.jl as well...

[bliang26]

Sure, I will try asking there.

[tkf]

I wonder what is in C:\Users\bliang26\.julia\packages\PackageCompiler\oT98U\sysimg\run_julia_code.jl, C:\Users\bliang26\.julia\packages\PackageCompiler\oT98U\sysimg\precompile.jl, and the files included from them (if any). It could be due to #192; i.e., PyCall.__init__ is not called before PyPlot.__init__. It would mean to call CPython API without initializing it and explain why there is a crash. A possible workaround would be to do compile_package("PyCall", "PyPlot"; force=false, reuse=false) although I'm not sure if it would work (I can't test this in my machine due to JuliaLang/julia#31156).

[bliang26]

The workaround helped but then I got the following error. By looking at #148 this seems to be related to global variables. After taking care of all global variables as suggested in #148 (I thought I did) in PyPlot.jl I still got the same error. Any ideas? Thanks.

fatal: error thrown and no exception handler available.
ErrorException("Task cannot be serialized")
rec_backtrace at /home/Administrator/buildbot/worker/package_win64/build/src\stackwalk.c:94
record_backtrace at /home/Administrator/buildbot/worker/package_win64/build/src\task.c:217 [inlined]
jl_throw at /home/Administrator/buildbot/worker/package_win64/build/src\task.c:417
jl_error at /home/Administrator/buildbot/worker/package_win64/build/src\rtutils.c:41
jl_serialize_value_ at /home/Administrator/buildbot/worker/package_win64/build/src\staticdata.c:294
jl_serialize_value_ at /home/Administrator/buildbot/worker/package_win64/build/src\staticdata.c:252 [inlined]
jl_serialize_value_ at /home/Administrator/buildbot/worker/package_win64/build/src\staticdata.c:286
jl_serialize_value_ at /home/Administrator/buildbot/worker/package_win64/build/src\julia.h:915 [inlined]
jl_serialize_value_ at /home/Administrator/buildbot/worker/package_win64/build/src\staticdata.c:303
jl_serialize_value_ at /home/Administrator/buildbot/worker/package_win64/build/src\julia.h:915 [inlined]
jl_serialize_value_ at /home/Administrator/buildbot/worker/package_win64/build/src\staticdata.c:303
jl_serialize_value_ at /home/Administrator/buildbot/worker/package_win64/build/src\staticdata.c:252 [inlined]
jl_serialize_value_ at /home/Administrator/buildbot/worker/package_win64/build/src\staticdata.c:286
jl_serialize_value_ at /home/Administrator/buildbot/worker/package_win64/build/src\julia.h:915 [inlined]
jl_serialize_value_ at /home/Administrator/buildbot/worker/package_win64/build/src\staticdata.c:303
jl_serialize_value_ at /home/Administrator/buildbot/worker/package_win64/build/src\staticdata.c:252 [inlined]
jl_serialize_module at /home/Administrator/buildbot/worker/package_win64/build/src\staticdata.c:230 [inlined]
jl_serialize_value_ at /home/Administrator/buildbot/worker/package_win64/build/src\staticdata.c:291
jl_serialize_value_ at /home/Administrator/buildbot/worker/package_win64/build/src\staticdata.c:252 [inlined]
jl_serialize_module at /home/Administrator/buildbot/worker/package_win64/build/src\staticdata.c:232 [inlined]
jl_serialize_value_ at /home/Administrator/buildbot/worker/package_win64/build/src\staticdata.c:291
jl_serialize_value_ at /home/Administrator/buildbot/worker/package_win64/build/src\staticdata.c:252 [inlined]
jl_serialize_module at /home/Administrator/buildbot/worker/package_win64/build/src\staticdata.c:230 [inlined]
jl_serialize_value_ at /home/Administrator/buildbot/worker/package_win64/build/src\staticdata.c:291
jl_serialize_module at /home/Administrator/buildbot/worker/package_win64/build/src\staticdata.c:222 [inlined]
jl_serialize_value_ at /home/Administrator/buildbot/worker/package_win64/build/src\staticdata.c:291
jl_serialize_value_ at /home/Administrator/buildbot/worker/package_win64/build/src\staticdata.c:337 [inlined]
jl_save_system_image_to_stream at /home/Administrator/buildbot/worker/package_win64/build/src\staticdata.c:1273
jl_create_system_image at /home/Administrator/buildbot/worker/package_win64/build/src\staticdata.c:1378
jl_write_compiler_output at /home/Administrator/buildbot/worker/package_win64/build/src\precompile.c:76
jl_atexit_hook at /home/Administrator/buildbot/worker/package_win64/build/src/home/Administrator/buildbot/worker/package_win64/build/src\init.c:222
wmain at /home/Administrator/buildbot/worker/package_win64/build/ui\repl.c:218
__tmainCRTStartup at /usr/src/debug/mingw64-x86_64-runtime-5.0.3-1/crt\crtexe.c:329
mainCRTStartup at /usr/src/debug/mingw64-x86_64-runtime-5.0.3-1/crt\crtexe.c:212
BaseThreadInitThunk at C:\WINDOWS\System32\KERNEL32.DLL (unknown line)
RtlUserThreadStart at C:\WINDOWS\SYSTEM32\ntdll.dll (unknown line)
ERROR: failed process: Process(`'C:\Users\bliang26\AppData\Local\Julia-1.1.0\bin\julia.exe' '--sysimage=C:\Users\bliang26\.julia\dev\PackageCompiler\sysimg\backup\native\sys.dll' --output-o=sys.a --track-allocation=none --code-coverage=none --history-file=yes --inline=yes --math-mode=ieee --compile=yes --track-allocation=none --sysimage-native-code=yes '--sysimage=C:\Users\bliang26\AppData\Local\Julia-1.1.0\lib\julia\sys.dll' --compiled-modules=yes --optimize=2 'C:\Users\bliang26\.julia\dev\PackageCompiler\sysimg\run_julia_code.jl'`, ProcessExited(1)) [1]
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 at .\process.jl:724 [inlined]
 [5] #run_julia#1 at C:\Users\bliang26\.julia\dev\PackageCompiler\src\compiler_flags.jl:225 [inlined]
 [6] #run_julia at .\none:0 [inlined]
 [7] (::getfield(PackageCompiler, Symbol("##13#14")){Base.Iterators.Pairs{Symbol,Any,NTuple{14,Symbol},NamedTuple{(:sysimage, :startup_file, :handle_signals, :sysimage_native_code, :compiled_modules, :depwarn, :warn_overwrite, :compile, :cpu_target, :optimize, :debug_level, :inline, :check_bounds, :math_mode),Tuple{String,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing}}},String})() at C:\Users\bliang26\.julia\dev\PackageCompiler\src\static_julia.jl:262
 [8] cd(::getfield(PackageCompiler, Symbol("##13#14")){Base.Iterators.Pairs{Symbol,Any,NTuple{14,Symbol},NamedTuple{(:sysimage, :startup_file, :handle_signals, :sysimage_native_code, :compiled_modules, :depwarn, :warn_overwrite, :compile, :cpu_target, :optimize, :debug_level, :inline, :check_bounds, :math_mode),Tuple{String,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing}}},String}, ::String) at .\file.jl:85
 [9] #build_object#12(::Base.Iterators.Pairs{Symbol,Any,NTuple{14,Symbol},NamedTuple{(:sysimage, :startup_file, :handle_signals, :sysimage_native_code, :compiled_modules, :depwarn, :warn_overwrite, :compile, :cpu_target, :optimize, :debug_level, :inline, :check_bounds, :math_mode),Tuple{String,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing}}}, ::Function, ::String, ::String, ::String, ::Bool) at C:\Users\bliang26\.julia\dev\PackageCompiler\src\static_julia.jl:261
 [10] #build_object at .\none:0 [inlined]
 [11] build_object(::String, ::String, ::String, ::Bool, ::String, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing) at C:\Users\bliang26\.julia\dev\PackageCompiler\src\static_julia.jl:240
 [12] #static_julia#5(::Nothing, ::Bool, ::Bool, ::String, ::String, ::Nothing, ::Bool, ::Bool, ::Bool, ::Bool, ::Bool, ::Bool, ::Bool, ::Bool, ::Nothing, ::Bool, ::Bool, ::String, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::typeof(static_julia), ::String) at C:\Users\bliang26\.julia\dev\PackageCompiler\src\static_julia.jl:161
 [13] #static_julia at .\none:0 [inlined]
 [14] #build_sysimg#29(::Bool, ::Bool, ::Bool, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::typeof(PackageCompiler.build_sysimg), ::String, ::String) at C:\Users\bliang26\.julia\dev\PackageCompiler\src\api.jl:25
 [15] #build_sysimg at .\none:0 [inlined]
 [16] #compile_package#67(::Bool, ::Bool, ::Bool, ::Nothing, ::Bool, ::Function, ::Tuple{String,String}, ::Vararg{Tuple{String,String},N} where N) at C:\Users\bliang26\.julia\dev\PackageCompiler\src\PackageCompiler.jl:130
 [17] (::getfield(PackageCompiler, Symbol("#kw##compile_package")))(::NamedTuple{(:force, :reuse),Tuple{Bool,Bool}}, ::typeof(compile_package), ::Tuple{String,String}, ::Vararg{Tuple{String,String},N} where N) at .\none:0
 [18] #compile_package#64(::Base.Iterators.Pairs{Symbol,Bool,Tuple{Symbol,Symbol},NamedTuple{(:force, :reuse),Tuple{Bool,Bool}}}, ::Function, ::String, ::Vararg{String,N} where N) at C:\Users\bliang26\.julia\dev\PackageCompiler\src\PackageCompiler.jl:94
 [19] (::getfield(PackageCompiler, Symbol("#kw##compile_package")))(::NamedTuple{(:force, :reuse),Tuple{Bool,Bool}}, ::typeof(compile_package), ::String, ::Vararg{String,N} where N) at .\none:0
 [20] top-level scope at none:0

[tkf]

Hmm... I guess it's something to do with the GUI event loop in PyCall (although I think we are stopping the event loop via atexit hook).

[tkf]

It looks like you can workaround this by ENV["MPLBACKEND"] = "agg".

I checked it with the following changes in PyCall:

$ git diff master
diff --git a/aot/compile.jl b/aot/compile.jl
index 63d0cb7..a71415d 100755
--- a/aot/compile.jl
+++ b/aot/compile.jl
@@ -9,6 +9,7 @@ Pkg.activate(@__DIR__)
 Pkg.add("MacroTools")
 Pkg.develop(PackageSpec(name="PyCall", path=dirname(@__DIR__)))
 Pkg.build("PyCall")
+Pkg.add("PyPlot")
 Pkg.activate()

 using PackageCompiler
diff --git a/aot/precompile.jl b/aot/precompile.jl
index cb63b73..4ba69e3 100644
--- a/aot/precompile.jl
+++ b/aot/precompile.jl
@@ -14,3 +14,6 @@ isdefined(MacroTools, :__init__) && MacroTools.__init__()
 using PyCall
 PyCall.__init__()
 PyCall.pyimport("sys")[:executable]
+
+using PyPlot
+PyPlot.__init__()

$ MPLBACKEND=agg aot/compile.jl --color=yes
...
[ Info: System image: /home/takafumi/.julia/dev/PyCall/aot/sys.so

So, this part seems to be an issue in PyCall and/or PyPlot.

[bliang26]

Awesome! How did you find out? The error message didn't show any clue. This definitely works, but the problem is that no figure shows up as I plot since the agg backend is for non-interactive use. If I switch to other interactive backends such as qt5agg I still got the same error message. Could you let me know how did you debug it so that maybe I can give it a try. Thanks.

[tkf]

How did you find out?

I thought Task cannot be serialized error was due to Task instance stored in some global state. PyCall uses Task (via Timer) for setting up GUI so I thought it could be solved by skipping the GUI setup in PyPlot (agg is the non-GUI backend).

the problem is that no figure shows up as I plot since the agg backend is for non-interactive use

I observe this too. The strange thing is that both matplotlib and PyPlot.jl report that they have the correct GUI backend. Also, re-starting the GUI with

using PyCall
pygui_stop_all()
pygui_start(:tk)  # pygui_start(:qt5) in your case

fixes the problem. I haven't figured out what is going on.

Could you let me know how did you debug it

At this point I think you need to debug PyCall.pygui_start (or qt_eventloop in your case) or something.

[KestutisMa]

It is working for me, just add show() at end.
I also modified first line runtests.jl of PyPlot to ENV["MPLBACKEND"]="qt"