ERROR: Failed to precompile PyCall

[kmundnic]

Hi,

I'm getting the following error:

ERROR: Failed to precompile PyCall to /Users/karel/.julia/lib/v0.5/PyCall.ji.
 in compilecache(::String) at ./loading.jl:593
 in require(::Symbol) at ./loading.jl:422
 in require(::Symbol) at /Applications/Julia-0.5.app/Contents/Resources/julia/lib/julia/sys.dylib:?

I have the following info

Julia Version 0.5.0
Commit 3c9d753 (2016-09-19 18:14 UTC)
Platform Info:
  System: Darwin (x86_64-apple-darwin13.4.0)
  CPU: Intel(R) Core(TM) i5-2415M CPU @ 2.30GHz
  WORD_SIZE: 64
  uname: Darwin 14.5.0 Darwin Kernel Version 14.5.0: Sun Sep 25 22:07:15 PDT 2016; root:xnu-2782.50.9~1/RELEASE_X86_64 x86_64 i386
Memory: 8.0 GB (253.6953125 MB free)
Uptime: 841779.0 sec
Load Avg:  2.7802734375  2.693359375  2.69482421875
Intel(R) Core(TM) i5-2415M CPU @ 2.30GHz: 
       speed         user         nice          sys         idle          irq
#1  2300 MHz    2143979 s          0 s     783761 s    2848735 s          0 s
#2  2300 MHz     629401 s          0 s     232240 s    4905198 s          0 s
#3  2300 MHz    2084304 s          0 s     670470 s    3012065 s          0 s
#4  2300 MHz     667471 s          0 s     240400 s    4858966 s          0 s

  BLAS: libopenblas (USE64BITINT DYNAMIC_ARCH NO_AFFINITY Sandybridge)
  LAPACK: libopenblas64_
  LIBM: libopenlibm
  LLVM: libLLVM-3.7.1 (ORCJIT, sandybridge)
Environment:
  TERM = xterm-256color
  PATH = /Applications/Julia-0.5.app/Contents/Resources/julia/bin:/Applications/Julia-0.5.0.app/Contents/Resources/julia/bin/julia:/Applications/MATLAB_R2016a.app/bin:/Users/karel/anaconda/bin:/Applications/Julia-0.5.app/Contents/Resources/julia/bin:/opt/local/bin:/opt/local/sbin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Library/TeX/texbin
  XPC_FLAGS = 0x0
  HOME = /Users/karel
  FONTCONFIG_PATH = /Applications/Julia-0.5.app/Contents/Resources/julia/etc/fonts

Package Directory: /Users/karel/.julia/v0.5
8 required packages:
 - Atom                          0.5.8
 - DataFrames                    0.8.5
 - MAT                           0.3.1
 - MATLAB                        0.5.0
 - NPZ                           0.2.0
 - Plots                         0.10.3
 - PyCall                        1.10.0
 - PyPlot                        2.3.1
62 additional packages:
 - ASTInterpreter                0.0.4
 - AbstractTrees                 0.0.4
 - ArgParse                      0.4.0
 - BinDeps                       0.4.5
 - Blink                         0.5.1
 - Blosc                         0.1.7
 - BufferedStreams               0.3.0
 - COFF                          0.0.2
 - CRC                           1.2.0
 - CodeTools                     0.4.3
 - Codecs                        0.2.0
 - ColorTypes                    0.3.2
 - Colors                        0.7.1
 - Compat                        0.16.2
 - Conda                         0.5.1
 - DWARF                         0.1.0
 - DataArrays                    0.3.12
 - DataStructures                0.5.2
 - ELF                           0.1.0
 - FileIO                        0.3.0
 - FixedPointNumbers             0.3.2
 - FixedSizeArrays               0.2.5
 - GZip                          0.2.20
 - Gallium                       0.0.4
 - HDF5                          0.7.3
 - Hiccup                        0.1.1
 - Homebrew                      0.4.2
 - HttpCommon                    0.2.6
 - HttpParser                    0.2.0
 - HttpServer                    0.1.7
 - Iterators                     0.2.0
 - JSON                          0.8.2
 - JuliaParser                   0.7.4
 - Juno                          0.2.5
 - LNR                           0.0.2
 - LaTeXStrings                  0.2.0
 - Lazy                          0.11.5
 - Libz                          0.2.3
 - MachO                         0.0.4
 - MacroTools                    0.3.5
 - MbedTLS                       0.4.3
 - Measures                      0.0.3
 - Media                         0.2.5
 - Mustache                      0.1.3
 - Mux                           0.2.3
 - ObjFileBase                   0.0.4
 - PlotThemes                    0.1.1
 - PlotUtils                     0.3.0
 - Reactive                      0.3.7
 - RecipesBase                   0.1.0
 - Reexport                      0.0.3
 - SHA                           0.3.1
 - Showoff                       0.0.7
 - SortingAlgorithms             0.1.0
 - StatsBase                     0.13.0
 - StructIO                      0.0.2
 - TerminalUI                    0.0.2
 - TextWrap                      0.1.6
 - URIParser                     0.1.8
 - VT100                         0.0.2
 - WebSockets                    0.2.1
 - ZipFile                       0.3.0

Any ideas?

[stevengj]

What is the output of Pkg.build("PyCall")?

[kmundnic]

INFO: Building Conda
INFO: Building PyCall
Fetching package metadata .........
Solving package specifications: .

# All requested packages already installed.
# packages in environment at /Users/karel/.julia/v0.5/Conda/deps/usr:
#
numpy                     1.12.0                   py27_0  
INFO: PyCall is using /Users/karel/.julia/v0.5/Conda/deps/usr/bin/python (Python 2.7.12) at /Users/karel/.julia/v0.5/Conda/deps/usr/bin/python, libpython = /Users/karel/.julia/v0.5/Conda/deps/usr/lib/libpython2.7
INFO: /Users/karel/.julia/v0.5/PyCall/deps/deps.jl has not changed
INFO: /Users/karel/.julia/v0.5/PyCall/deps/PYTHON has not changed

[stevengj]

Weird. There is no other output from using PyCall?

[kmundnic]

Here's all the output from using PyCall:

julia> using PyCall
INFO: Precompiling module PyCall.

signal (11): Segmentation fault: 11
while loading /Users/karel/.julia/v0.5/PyCall/src/pyclass.jl, in expression starting on line 45
julia_type_to_llvm at /Users/osx/buildbot/slave/package_osx10_9-x64/build/src/./cgutils.cpp:318
mark_julia_const at /Users/osx/buildbot/slave/package_osx10_9-x64/build/src/codegen.cpp:641 [inlined]
emit_expr at /Users/osx/buildbot/slave/package_osx10_9-x64/build/src/codegen.cpp:3140
emit_invoke at /Users/osx/buildbot/slave/package_osx10_9-x64/build/src/codegen.cpp:2669 [inlined]
emit_expr at /Users/osx/buildbot/slave/package_osx10_9-x64/build/src/codegen.cpp:3162
emit_jlcall at /Users/osx/buildbot/slave/package_osx10_9-x64/build/src/codegen.cpp:2578
emit_call at /Users/osx/buildbot/slave/package_osx10_9-x64/build/src/codegen.cpp:2739
emit_expr at /Users/osx/buildbot/slave/package_osx10_9-x64/build/src/codegen.cpp:3172
emit_function at /Users/osx/buildbot/slave/package_osx10_9-x64/build/src/codegen.cpp:4691
jl_compile_linfo at /Users/osx/buildbot/slave/package_osx10_9-x64/build/src/codegen.cpp:809
jl_compile_for_dispatch at /Users/osx/buildbot/slave/package_osx10_9-x64/build/src/gf.c:1310
jl_call_method_internal at /Users/osx/buildbot/slave/package_osx10_9-x64/build/src/./julia_internal.h:184 [inlined]
jl_apply_generic at /Users/osx/buildbot/slave/package_osx10_9-x64/build/src/gf.c:1942
@capture at /Users/karel/.julia/v0.5/MacroTools/src/macro.jl:61
jl_call_method_internal at /Users/osx/buildbot/slave/package_osx10_9-x64/build/src/./julia_internal.h:189 [inlined]
fl_invoke_julia_macro at /Users/osx/buildbot/slave/package_osx10_9-x64/build/src/ast.c:161
apply_cl at /Users/osx/buildbot/slave/package_osx10_9-x64/build/src/flisp/flisp.c:1227
_applyn at /Users/osx/buildbot/slave/package_osx10_9-x64/build/src/flisp/flisp.c:678
fl_map1 at /Users/osx/buildbot/slave/package_osx10_9-x64/build/src/flisp/flisp.c:2220
apply_cl at /Users/osx/buildbot/slave/package_osx10_9-x64/build/src/flisp/flisp.c:1177
_applyn at /Users/osx/buildbot/slave/package_osx10_9-x64/build/src/flisp/flisp.c:678
fl_map1 at /Users/osx/buildbot/slave/package_osx10_9-x64/build/src/flisp/flisp.c:2220
apply_cl at /Users/osx/buildbot/slave/package_osx10_9-x64/build/src/flisp/flisp.c:1177
_applyn at /Users/osx/buildbot/slave/package_osx10_9-x64/build/src/flisp/flisp.c:678
fl_map1 at /Users/osx/buildbot/slave/package_osx10_9-x64/build/src/flisp/flisp.c:2220
apply_cl at /Users/osx/buildbot/slave/package_osx10_9-x64/build/src/flisp/flisp.c:1177
do_trycatch at /Users/osx/buildbot/slave/package_osx10_9-x64/build/src/flisp/flisp.c:899
apply_cl at /Users/osx/buildbot/slave/package_osx10_9-x64/build/src/flisp/flisp.c:1807
_applyn at /Users/osx/buildbot/slave/package_osx10_9-x64/build/src/flisp/flisp.c:678
fl_applyn at /Users/osx/buildbot/slave/package_osx10_9-x64/build/src/flisp/flisp.c:723
jl_parse_eval_all at /Users/osx/buildbot/slave/package_osx10_9-x64/build/src/ast.c:702
jl_load at /Users/osx/buildbot/slave/package_osx10_9-x64/build/src/toplevel.c:596 [inlined]
jl_load_ at /Users/osx/buildbot/slave/package_osx10_9-x64/build/src/toplevel.c:605
include_from_node1 at ./loading.jl:488
jlcall_include_from_node1_20125 at /Applications/Julia-0.5.app/Contents/Resources/julia/lib/julia/sys.dylib (unknown line)
jl_call_method_internal at /Users/osx/buildbot/slave/package_osx10_9-x64/build/src/./julia_internal.h:189 [inlined]
jl_apply_generic at /Users/osx/buildbot/slave/package_osx10_9-x64/build/src/gf.c:1942
do_call at /Users/osx/buildbot/slave/package_osx10_9-x64/build/src/interpreter.c:66
eval at /Users/osx/buildbot/slave/package_osx10_9-x64/build/src/interpreter.c:190
jl_toplevel_eval_flex at /Users/osx/buildbot/slave/package_osx10_9-x64/build/src/toplevel.c:558
jl_eval_module_expr at /Users/osx/buildbot/slave/package_osx10_9-x64/build/src/toplevel.c:196
jl_toplevel_eval_flex at /Users/osx/buildbot/slave/package_osx10_9-x64/build/src/toplevel.c:465
jl_parse_eval_all at /Users/osx/buildbot/slave/package_osx10_9-x64/build/src/ast.c:717
jl_load at /Users/osx/buildbot/slave/package_osx10_9-x64/build/src/toplevel.c:596 [inlined]
jl_load_ at /Users/osx/buildbot/slave/package_osx10_9-x64/build/src/toplevel.c:605
include_from_node1 at ./loading.jl:488
jlcall_include_from_node1_20125 at /Applications/Julia-0.5.app/Contents/Resources/julia/lib/julia/sys.dylib (unknown line)
jl_call_method_internal at /Users/osx/buildbot/slave/package_osx10_9-x64/build/src/./julia_internal.h:189 [inlined]
jl_apply_generic at /Users/osx/buildbot/slave/package_osx10_9-x64/build/src/gf.c:1942
do_call at /Users/osx/buildbot/slave/package_osx10_9-x64/build/src/interpreter.c:66
eval at /Users/osx/buildbot/slave/package_osx10_9-x64/build/src/interpreter.c:190
jl_toplevel_eval_flex at /Users/osx/buildbot/slave/package_osx10_9-x64/build/src/toplevel.c:558
jl_toplevel_eval_in_warn at /Users/osx/buildbot/slave/package_osx10_9-x64/build/src/builtins.c:590
macro expansion; at ./none:2 [inlined]
anonymous at ./<missing> (unknown line)
unknown function (ip: 0x314c586c1)
jl_call_method_internal at /Users/osx/buildbot/slave/package_osx10_9-x64/build/src/./julia_internal.h:189 [inlined]
jl_toplevel_eval_flex at /Users/osx/buildbot/slave/package_osx10_9-x64/build/src/toplevel.c:569
jl_toplevel_eval_in_warn at /Users/osx/buildbot/slave/package_osx10_9-x64/build/src/builtins.c:590
eval at ./boot.jl:234
jlcall_eval_19752 at /Applications/Julia-0.5.app/Contents/Resources/julia/lib/julia/sys.dylib (unknown line)
jl_call_method_internal at /Users/osx/buildbot/slave/package_osx10_9-x64/build/src/./julia_internal.h:189 [inlined]
jl_apply_generic at /Users/osx/buildbot/slave/package_osx10_9-x64/build/src/gf.c:1942
process_options at ./client.jl:239
_start at ./client.jl:318
jlcall__start_21452 at /Applications/Julia-0.5.app/Contents/Resources/julia/lib/julia/sys.dylib (unknown line)
jl_call_method_internal at /Users/osx/buildbot/slave/package_osx10_9-x64/build/src/./julia_internal.h:189 [inlined]
jl_apply_generic at /Users/osx/buildbot/slave/package_osx10_9-x64/build/src/gf.c:1942
true_main at /Applications/Julia-0.5.app/Contents/Resources/julia/bin/julia (unknown line)
main at /Applications/Julia-0.5.app/Contents/Resources/julia/bin/julia (unknown line)
Allocations: 1824293 (Pool: 1823419; Big: 874); GC: 0
ERROR: Failed to precompile PyCall to /Users/karel/.julia/lib/v0.5/PyCall.ji.
 in compilecache(::String) at ./loading.jl:593
 in require(::Symbol) at ./loading.jl:422
 in require(::Symbol) at /Applications/Julia-0.5.app/Contents/Resources/julia/lib/julia/sys.dylib:?

[stevengj]

Okay, I can reproduce the problem after doing a Pkg.update().

[kmundnic]

@stevengj, any way I can go back and precompile with a previous (working) version?

Thanks for your help!

[stevengj]

Pkg.pin("MacroTools", v"0.3.4") works around the problem for me.

[kmundnic]

Thanks!

[mmikhasenko]

Was the problem solved in 2017?

I am getting something similar now with julia-1.7

[MalteBoehm]

I am getting it when i build a linux Docker with julia. Very annoying

[sibyjackgrove]

@MalteBoehm were you able to find a solution for linux Docker with Julia?

[thierrymoudiki]

@stevengj @sibyjackgrove Using Julia v1.9 on Ubuntu, getting ERROR: LoadError: Failed to precompile PyCall when running using PyCall (worked last week). Has anyone been able to solve this error in 2023?