Hi Julia folks,
I’m running into a strange issue using Turing.jl. I do most of my work in Atom, where Turing works just fine. However, recently I’ve been getting the following error below upon running using Turing in Jupyter notebooks. This is particularly weird because I know I’ve successfully used Turing in a Jupyter notebook before. Upgrading from Julia 1.7.2 to 1.8.5 hasn’t fixed the problem.
I’d greatly appreciate any suggestions for what the problem might be and how to fix it!
Best wishes,
-ADM
Error:
[ Info: Precompiling Turing [fce5fe82-541a-59a6-adf8-730c64b5f9a0]
WARNING: using AbstractTrees.isroot in module LeftChildRightSiblingTrees conflicts with an existing identifier.
ERROR: LoadError: UndefVarError: parentlinks not defined
Stacktrace:
[1] getproperty(x::Module, f::Symbol)
@ Base ./Base.jl:31
[2] top-level scope
@ ~/.julia/packages/LeftChildRightSiblingTrees/FaxpE/src/abstracttrees.jl:10
[3] include(mod::Module, _path::String)
@ Base ./Base.jl:419
[4] include(x::String)
@ LeftChildRightSiblingTrees ~/.julia/packages/LeftChildRightSiblingTrees/FaxpE/src/LeftChildRightSiblingTrees.jl:1
[5] top-level scope
@ ~/.julia/packages/LeftChildRightSiblingTrees/FaxpE/src/LeftChildRightSiblingTrees.jl:248
[6] include
@ ./Base.jl:419 [inlined]
[7] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt64}}, source::String)
@ Base ./loading.jl:1554
[8] top-level scope
@ stdin:1
in expression starting at /Users/alexandermeyer/.julia/packages/LeftChildRightSiblingTrees/FaxpE/src/abstracttrees.jl:10
in expression starting at /Users/alexandermeyer/.julia/packages/LeftChildRightSiblingTrees/FaxpE/src/LeftChildRightSiblingTrees.jl:1
in expression starting at stdin:1
ERROR: LoadError: Failed to precompile LeftChildRightSiblingTrees [1d6d02ad-be62-4b6b-8a6d-2f90e265016e] to /Users/alexandermeyer/.julia/compiled/v1.8/LeftChildRightSiblingTrees/jl_d01P6m.
Stacktrace:
[1] error(s::String)
@ Base ./error.jl:35
[2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool)
@ Base ./loading.jl:1707
[3] compilecache
@ ./loading.jl:1651 [inlined]
[4] _require(pkg::Base.PkgId)
@ Base ./loading.jl:1337
[5] _require_prelocked(uuidkey::Base.PkgId)
@ Base ./loading.jl:1200
[6] macro expansion
@ ./loading.jl:1180 [inlined]
[7] macro expansion
@ ./lock.jl:223 [inlined]
[8] require(into::Module, mod::Symbol)
@ Base ./loading.jl:1144
[9] include
@ ./Base.jl:419 [inlined]
[10] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt64}}, source::String)
@ Base ./loading.jl:1554
[11] top-level scope
@ stdin:1
in expression starting at /Users/alexandermeyer/.julia/packages/TerminalLoggers/7fg8U/src/TerminalLoggers.jl:1
in expression starting at stdin:1
ERROR: LoadError: Failed to precompile TerminalLoggers [5d786b92-1e48-4d6f-9151-6b4477ca9bed] to /Users/alexandermeyer/.julia/compiled/v1.8/TerminalLoggers/jl_VJILu3.
Stacktrace:
[1] error(s::String)
@ Base ./error.jl:35
[2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool)
@ Base ./loading.jl:1707
[3] compilecache
@ ./loading.jl:1651 [inlined]
[4] _require(pkg::Base.PkgId)
@ Base ./loading.jl:1337
[5] _require_prelocked(uuidkey::Base.PkgId)
@ Base ./loading.jl:1200
[6] macro expansion
@ ./loading.jl:1180 [inlined]
[7] macro expansion
@ ./lock.jl:223 [inlined]
[8] require(into::Module, mod::Symbol)
@ Base ./loading.jl:1144
[9] include
@ ./Base.jl:419 [inlined]
[10] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt64}}, source::String)
@ Base ./loading.jl:1554
[11] top-level scope
@ stdin:1
in expression starting at /Users/alexandermeyer/.julia/packages/AbstractMCMC/F9Hbk/src/AbstractMCMC.jl:1
in expression starting at stdin:1
ERROR: LoadError: Failed to precompile AbstractMCMC [80f14c24-f653-4e6a-9b94-39d6b0f70001] to /Users/alexandermeyer/.julia/compiled/v1.8/AbstractMCMC/jl_Q7eGMn.
Stacktrace:
[1] error(s::String)
@ Base ./error.jl:35
[2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool)
@ Base ./loading.jl:1707
[3] compilecache
@ ./loading.jl:1651 [inlined]
[4] _require(pkg::Base.PkgId)
@ Base ./loading.jl:1337
[5] _require_prelocked(uuidkey::Base.PkgId)
@ Base ./loading.jl:1200
[6] macro expansion
@ ./loading.jl:1180 [inlined]
[7] macro expansion
@ ./lock.jl:223 [inlined]
[8] require(into::Module, mod::Symbol)
@ Base ./loading.jl:1144
[9] include
@ ./Base.jl:419 [inlined]
[10] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt64}}, source::String)
@ Base ./loading.jl:1554
[11] top-level scope
@ stdin:1
in expression starting at /Users/alexandermeyer/.julia/packages/MCMCChains/9On2K/src/MCMCChains.jl:1
in expression starting at stdin:1
ERROR: LoadError: Failed to precompile MCMCChains [c7f686f2-ff18-58e9-bc7b-31028e88f75d] to /Users/alexandermeyer/.julia/compiled/v1.8/MCMCChains/jl_aQJxsV.
Stacktrace:
[1] error(s::String)
@ Base ./error.jl:35
[2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool)
@ Base ./loading.jl:1707
[3] compilecache
@ ./loading.jl:1651 [inlined]
[4] _require(pkg::Base.PkgId)
@ Base ./loading.jl:1337
[5] _require_prelocked(uuidkey::Base.PkgId)
@ Base ./loading.jl:1200
[6] macro expansion
@ ./loading.jl:1180 [inlined]
[7] macro expansion
@ ./lock.jl:223 [inlined]
[8] require(into::Module, mod::Symbol)
@ Base ./loading.jl:1144
[9] include
@ ./Base.jl:419 [inlined]
[10] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt64}}, source::Nothing)
@ Base ./loading.jl:1554
[11] top-level scope
@ stdin:1
in expression starting at /Users/alexandermeyer/.julia/packages/Turing/Suzsv/src/Turing.jl:1
in expression starting at stdin:1
Failed to precompile Turing [fce5fe82-541a-59a6-adf8-730c64b5f9a0] to /Users/alexandermeyer/.julia/compiled/v1.8/Turing/jl_M4o9IV.
Stacktrace:
[1] error(s::String)
@ Base ./error.jl:35
[2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool)
@ Base ./loading.jl:1707
[3] compilecache
@ ./loading.jl:1651 [inlined]
[4] _require(pkg::Base.PkgId)
@ Base ./loading.jl:1337
[5] _require_prelocked(uuidkey::Base.PkgId)
@ Base ./loading.jl:1200
[6] macro expansion
@ ./loading.jl:1180 [inlined]
[7] macro expansion
@ ./lock.jl:223 [inlined]
[8] require(into::Module, mod::Symbol)
@ Base ./loading.jl:1144