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Julia crash on load(“RDatasets”) with "Invalid constantexpr cast!" linking or compilation error? #18

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AlexMikhalev opened this issue Dec 3, 2012 · 22 comments

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@AlexMikhalev
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brew tap staticfloat/julia
brew install --HEAD julia

edited sparse-suite by copy paste from tap as tapping failed
brew edit suite-sparse

then:
brew install suite-sparse
brew install --HEAD julia
brew test -v julia
julia
_ _ ()_ | A fresh approach to technical computing
() | () () | Documentation: http://docs.julialang.org
_ _ | | __ _ | Type “help()” to list help topics
| | | | | | |/ ` | |
| | |
| | | | (
| | | Version 0.0.0+103529310.r2458.dirty
/ |_|||__’| | Commit 2458fa9da4 (2012-12-03 09:47:36)*
|__/ |

julia> load(“RDatasets”)

Warning: redefinition of constant NARule ignored.
Assertion failed: (CastInst::castIsValid(opc, C, Ty) && “Invalid constantexpr cast!”), function getCast, file Constants.cpp, line 1366.
Illegal instruction: 4

I was wondering if it's linking error?
what can I do to clean it?

@StefanKarpinski
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@staticfloat: this looks like it would be solved by a make cleanall if this were from a source installation, but I don't know how homebrew works well enough to say what to do here.

@staticfloat
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You should never have to do a make cleanall via Homebrew. Homebrew builds from a fresh git checkout every time. I'm updating my julia to the latest to see if I can reproduce.

@staticfloat
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I can reproduce, and can confirm that this is a Homebrew-specific problem. It looks like llvm is unhappy about something:

julia> load("RDatasets")
Warning: redefinition of constant NARule ignored.
Assertion failed: (CastInst::castIsValid(opc, C, Ty) && "Invalid constantexpr cast!"), function getCast, file Constants.cpp, line 1366.

Program received signal SIGABRT, Aborted.
0x00007fff88921212 in __pthread_kill ()
(gdb) bt
#0  0x00007fff88921212 in __pthread_kill ()
#1  0x00007fff8a1c7af4 in pthread_kill ()
#2  0x00000001007041f2 in abort ()
#3  0x00000001007041c0 in __assert_rtn ()
#4  0x000000010063f002 in llvm::ConstantExpr::getCast ()
#5  0x000000010007c40d in llvm::IRBuilder<true, llvm::ConstantFolder, llvm::IRBuilderDefaultInserter<true> >::CreateCast ()
#6  0x0000000100077215 in generic_box ()
#7  0x000000010006c355 in emit_intrinsic ()
#8  0x00000001000686cb in emit_known_call ()
#9  0x0000000100066e46 in emit_call ()
#10 0x0000000100063f6d in emit_expr ()
#11 0x000000010006401c in emit_expr ()
#12 0x0000000100060ad9 in emit_function ()
#13 0x0000000100052c99 in to_function ()
#14 0x0000000100052c10 in jl_compile ()
#15 0x0000000100050035 in jl_trampoline ()
#16 0x000000010008c3fe in jl_toplevel_eval_flex ()
#17 0x000000010008c230 in jl_toplevel_eval_flex ()
#18 0x000000010008ca05 in jl_parse_eval_all ()
#19 0x000000010008cbf8 in jl_load_ ()
#20 0x0000000101f568a7 in ?? ()
#21 0x0000000101f565d0 in ?? ()
#22 0x0000000100049b48 in jl_apply_generic ()
#23 0x0000000100082284 in do_call ()
#24 0x000000010008131a in eval ()
#25 0x000000010008c434 in jl_toplevel_eval_flex ()
#26 0x000000010008bf52 in jl_eval_module_expr ()
#27 0x000000010008c103 in jl_toplevel_eval_flex ()
#28 0x000000010008ca05 in jl_parse_eval_all ()
#29 0x000000010008cbf8 in jl_load_ ()
#30 0x0000000101f568a7 in ?? ()
#31 0x0000000101f565d0 in ?? ()
#32 0x0000000100049b48 in jl_apply_generic ()
#33 0x0000000100082284 in do_call ()
#34 0x000000010008131a in eval ()
#35 0x000000010008c434 in jl_toplevel_eval_flex ()
#36 0x000000010008ca05 in jl_parse_eval_all ()
#37 0x000000010008cbf8 in jl_load_ ()
#38 0x0000000101f568a7 in ?? ()
#39 0x0000000101f56bc3 in ?? ()
#40 0x0000000101f565d0 in ?? ()
#41 0x0000000100049b48 in jl_apply_generic ()
#42 0x0000000100082284 in do_call ()
#43 0x000000010008131a in eval ()
#44 0x000000010008c434 in jl_toplevel_eval_flex ()
#45 0x000000010004e597 in jl_f_top_eval ()
#46 0x0000000101f54fa2 in ?? ()
#47 0x0000000101f54c8b in ?? ()
#48 0x0000000100049b48 in jl_apply_generic ()
#49 0x0000000101f0125d in ?? ()
#50 0x0000000101f00f2e in ?? ()
#51 0x0000000101f00260 in ?? ()
#52 0x0000000100049b48 in jl_apply_generic ()
#53 0x00000001000018e8 in true_main ()
#54 0x0000000100086053 in julia_trampoline ()
#55 0x0000000100001b72 in main ()

I don't think I have the llvm expertise to debug this; could this be a library issue? (e.g. not finding a shared library at runtime) The fact that the homebrew formula breaks whereas a straight-up compile works is suspicious.

@StefanKarpinski
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cc: @JeffBezanson, @vtjnash for LLVM expertise.

@vtjnash
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vtjnash commented Dec 3, 2012

Can you build / install / run the debug version? Pending Jeff already knowing exactly what this comes from, it would help to be able to see line numbers above.

@AlexMikhalev
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Just in case it will be useful - I cloned recent julia repo and compiled it successfully via
git clone git://github.com/JuliaLang/julia.git
cd julia/
make

LLVM:
brew info llvm
llvm: stable 3.1 (bottled), HEAD
http://llvm.org/
/usr/local/Cellar/llvm/3.1 (768 files, 121M) *
Installed with: --all-targets
https://github.com/mxcl/homebrew/commits/master/Library/Formula/llvm.rb
==> Options
--shared
Build LLVM as a shared library
--universal
Build a universal binary
--with-clang
Build Clang C/ObjC/C++ frontend
--all-targets
Build all target backends
--rtti
Build with C++ RTTI
==> Caveats
Extra tools and bindings are installed in /usr/local/Cellar/llvm/3.1/share/llvm and /usr/local/Cellar/llvm/3.1/share/clang.

If you already have LLVM installed, then "brew upgrade llvm" might not work.
Instead, try:
brew rm llvm && brew install llvm

so it seems like there is something with dependencies - sparce-suite etc.

@staticfloat
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Here you go, @vtjnash

@StefanKarpinski
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@AlexMikhalev, while you're waiting on this, you may want to install from source. It takes a bit of time and isn't as convenient as homebrew, but it's a pretty solid process at this point this is likely to "just work".

@vtjnash
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vtjnash commented Dec 3, 2012

Its possible one of the dependancies is corrupting the stack / other memory somewhere along the way. I would probably have to walk this in a debugger to see how generic_box is calling CreateBitCast

@staticfloat
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@vtjnash; This is related to JuliaLang/julia#1694. Homebrew, by default, compiles LLVM with assertions enabled, which is the opposite of both Julia and MacPorts. I'm not sure if these assertions are causing the error, or if there are errors that are going uncaught in Julia, or if these are just warnings that we're fine with letting slip, but this is the cause of the problem.

@AlexMikhalev; I've submitted a pull request to Homebrew-main adding a --disable-assertions option to the llvm formula. Once it's accepted, you can just brew rm llvm; brew install llvm --disable-assertions and everything should work fine.

@staticfloat
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Note that although JuliaLang/julia#1694 is closed, this issue persists as long as llvm has been compiled without the --disable-assertions configure flag.

@samueljohn
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But didn't they fixed that assertion in their master branch? Does this formula checkout another branch?

@staticfloat
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This assertion is a different one, and I wanted to make sure people realized that.

@samueljohn
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I suck.

But still, I guess it's better not to wait for --disable-assertions but to fix the cause of the assertion, because it might truly be a bug in RDatasets or julia.

@staticfloat
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But still, I guess it's better not to wait for --disable-assertions but to fix the cause of the assertion, because it might truly be a bug in RDatasets or julia.

Agreed. :)

I suck.

Disagreed. :)

@vtjnash
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vtjnash commented Dec 7, 2012

This happens because these two lines cause a size mismatch (in box), where enum expects to create a 64 bit integer, but can't because an 8 bit integer of the same name already exists.

bitstype 8 NARule
@enum NARule KEEP FILTER REPLACE

(edit: from DataFrames/src/datavec.jl)

@staticfloat
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I just noticed that this happens when loading DataFrame as well, I think @vtjnash beat me to the punch though.

@staticfloat
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This should be solved now, whether your llvm installation is installed with assertions or not. @AlexMikhalev, are you still experiencing this error?

@AlexMikhalev
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No, error is now different:
brew doctor
brew info suite-sparse
brew install --HEAD julia
brew test -v julia
julia

julia> load("RDatasets")
Warning: New definition +(BitArray{N},AbstractArray{T,N}) at /usr/local/Cellar/julia/HEAD/share/julia/base/bitarray.jl:992 is ambiguous with +(AbstractArray{T,N},BitArray{N}) at bitarray.jl:993.
Make sure +(BitArray{N},BitArray{N}) is defined first.
Warning: New definition +(AbstractArray{T,N},BitArray{N}) at /usr/local/Cellar/julia/HEAD/share/julia/base/bitarray.jl:993 is ambiguous with +(BitArray{N},AbstractArray{T,N}) at bitarray.jl:992.
Make sure +(BitArray{N},BitArray{N}) is defined first.
Warning: New definition -(BitArray{N},AbstractArray{T,N}) at /usr/local/Cellar/julia/HEAD/share/julia/base/bitarray.jl:992 is ambiguous with -(AbstractArray{T,N},BitArray{N}) at bitarray.jl:993.
Make sure -(BitArray{N},BitArray{N}) is defined first.
Warning: New definition -(AbstractArray{T,N},BitArray{N}) at /usr/local/Cellar/julia/HEAD/share/julia/base/bitarray.jl:993 is ambiguous with -(BitArray{N},AbstractArray{T,N}) at bitarray.jl:992.
Make sure -(BitArray{N},BitArray{N}) is defined first.
Warning: New definition div(BitArray{N},AbstractArray{T,N}) at /usr/local/Cellar/julia/HEAD/share/julia/base/bitarray.jl:992 is ambiguous with div(AbstractArray{T,N},BitArray{N}) at bitarray.jl:993.
Make sure div(BitArray{N},BitArray{N}) is defined first.
Warning: New definition div(AbstractArray{T,N},BitArray{N}) at /usr/local/Cellar/julia/HEAD/share/julia/base/bitarray.jl:993 is ambiguous with div(BitArray{N},AbstractArray{T,N}) at bitarray.jl:992.
Make sure div(BitArray{N},BitArray{N}) is defined first.
Warning: New definition mod(BitArray{N},AbstractArray{T,N}) at /usr/local/Cellar/julia/HEAD/share/julia/base/bitarray.jl:992 is ambiguous with mod(AbstractArray{T,N},BitArray{N}) at bitarray.jl:993.
Make sure mod(BitArray{N},BitArray{N}) is defined first.
Warning: New definition mod(AbstractArray{T,N},BitArray{N}) at /usr/local/Cellar/julia/HEAD/share/julia/base/bitarray.jl:993 is ambiguous with mod(BitArray{N},AbstractArray{T,N}) at bitarray.jl:992.
Make sure mod(BitArray{N},BitArray{N}) is defined first.
Warning: New definition ./(BitArray{N},AbstractArray{T,N}) at /usr/local/Cellar/julia/HEAD/share/julia/base/bitarray.jl:992 is ambiguous with ./(AbstractArray{T,N},BitArray{N}) at bitarray.jl:993.
Make sure ./(BitArray{N},BitArray{N}) is defined first.
Warning: New definition ./(AbstractArray{T,N},BitArray{N}) at /usr/local/Cellar/julia/HEAD/share/julia/base/bitarray.jl:993 is ambiguous with ./(BitArray{N},AbstractArray{T,N}) at bitarray.jl:992.
Make sure ./(BitArray{N},BitArray{N}) is defined first.
Warning: New definition .^(BitArray{N},AbstractArray{T,N}) at /usr/local/Cellar/julia/HEAD/share/julia/base/bitarray.jl:992 is ambiguous with .^(AbstractArray{T,N},BitArray{N}) at bitarray.jl:993.
Make sure .^(BitArray{N},BitArray{N}) is defined first.
Warning: New definition .^(AbstractArray{T,N},BitArray{N}) at /usr/local/Cellar/julia/HEAD/share/julia/base/bitarray.jl:993 is ambiguous with .^(BitArray{N},AbstractArray{T,N}) at bitarray.jl:992.
Make sure .^(BitArray{N},BitArray{N}) is defined first.
Warning: New definition .(BitArray{N},AbstractArray{T,N}) at /usr/local/Cellar/julia/HEAD/share/julia/base/bitarray.jl:992 is ambiguous with .(AbstractArray{T,N},BitArray{N}) at bitarray.jl:993.
Make sure .(BitArray{N},BitArray{N}) is defined first.
Warning: New definition .
(AbstractArray{T,N},BitArray{N}) at /usr/local/Cellar/julia/HEAD/share/julia/base/bitarray.jl:993 is ambiguous with .(BitArray{N},AbstractArray{T,N}) at bitarray.jl:992.
Make sure .
(BitArray{N},BitArray{N}) is defined first.
Warning: New definition &(BitArray{N},AbstractArray{T,N}) at /usr/local/Cellar/julia/HEAD/share/julia/base/bitarray.jl:992 is ambiguous with &(AbstractArray{T,N},BitArray{N}) at bitarray.jl:993.
Make sure &(BitArray{N},BitArray{N}) is defined first.
Warning: New definition &(AbstractArray{T,N},BitArray{N}) at /usr/local/Cellar/julia/HEAD/share/julia/base/bitarray.jl:993 is ambiguous with &(BitArray{N},AbstractArray{T,N}) at bitarray.jl:992.
Make sure &(BitArray{N},BitArray{N}) is defined first.
Warning: New definition |(BitArray{N},AbstractArray{T,N}) at /usr/local/Cellar/julia/HEAD/share/julia/base/bitarray.jl:992 is ambiguous with |(AbstractArray{T,N},BitArray{N}) at bitarray.jl:993.
Make sure |(BitArray{N},BitArray{N}) is defined first.
Warning: New definition |(AbstractArray{T,N},BitArray{N}) at /usr/local/Cellar/julia/HEAD/share/julia/base/bitarray.jl:993 is ambiguous with |(BitArray{N},AbstractArray{T,N}) at bitarray.jl:992.
Make sure |(BitArray{N},BitArray{N}) is defined first.
Warning: New definition $(BitArray{N},AbstractArray{T,N}) at /usr/local/Cellar/julia/HEAD/share/julia/base/bitarray.jl:992 is ambiguous with $(AbstractArray{T,N},BitArray{N}) at bitarray.jl:993.
Make sure $(BitArray{N},BitArray{N}) is defined first.
Warning: New definition $(AbstractArray{T,N},BitArray{N}) at /usr/local/Cellar/julia/HEAD/share/julia/base/bitarray.jl:993 is ambiguous with $(BitArray{N},AbstractArray{T,N}) at bitarray.jl:992.
Make sure $(BitArray{N},BitArray{N}) is defined first.
Warning: Method definition .==(AbstractArray{T,N},AbstractArray{T,N}) in module Base at bitarray.jl:1009 overwritten in module DataFrames at /usr/local/Cellar/julia/HEAD/share/julia/base/bitarray.jl:1009.
Warning: Method definition .==(Any,AbstractArray{T,N}) in module Base at bitarray.jl:1016 overwritten in module DataFrames at /usr/local/Cellar/julia/HEAD/share/julia/base/bitarray.jl:1016.
Warning: Method definition .==(AbstractArray{T,N},Any) in module Base at bitarray.jl:1023 overwritten in module DataFrames at /usr/local/Cellar/julia/HEAD/share/julia/base/bitarray.jl:1023.
Warning: Method definition .<(AbstractArray{T,N},AbstractArray{T,N}) in module Base at bitarray.jl:1009 overwritten in module DataFrames at /usr/local/Cellar/julia/HEAD/share/julia/base/bitarray.jl:1009.
Warning: Method definition .<(Any,AbstractArray{T,N}) in module Base at bitarray.jl:1016 overwritten in module DataFrames at /usr/local/Cellar/julia/HEAD/share/julia/base/bitarray.jl:1016.
Warning: Method definition .<(AbstractArray{T,N},Any) in module Base at bitarray.jl:1023 overwritten in module DataFrames at /usr/local/Cellar/julia/HEAD/share/julia/base/bitarray.jl:1023.
Warning: Method definition .!=(AbstractArray{T,N},AbstractArray{T,N}) in module Base at bitarray.jl:1009 overwritten in module DataFrames at /usr/local/Cellar/julia/HEAD/share/julia/base/bitarray.jl:1009.
Warning: Method definition .!=(Any,AbstractArray{T,N}) in module Base at bitarray.jl:1016 overwritten in module DataFrames at /usr/local/Cellar/julia/HEAD/share/julia/base/bitarray.jl:1016.
Warning: Method definition .!=(AbstractArray{T,N},Any) in module Base at bitarray.jl:1023 overwritten in module DataFrames at /usr/local/Cellar/julia/HEAD/share/julia/base/bitarray.jl:1023.
Warning: Method definition .<=(AbstractArray{T,N},AbstractArray{T,N}) in module Base at bitarray.jl:1009 overwritten in module DataFrames at /usr/local/Cellar/julia/HEAD/share/julia/base/bitarray.jl:1009.
Warning: Method definition .<=(Any,AbstractArray{T,N}) in module Base at bitarray.jl:1016 overwritten in module DataFrames at /usr/local/Cellar/julia/HEAD/share/julia/base/bitarray.jl:1016.
Warning: Method definition .<=(AbstractArray{T,N},Any) in module Base at bitarray.jl:1023 overwritten in module DataFrames at /usr/local/Cellar/julia/HEAD/share/julia/base/bitarray.jl:1023.
Warning: New definition ==(BitArray{N},AbstractArray{Bool,N}) at /usr/local/Cellar/julia/HEAD/share/julia/base/bitarray.jl:1061 is ambiguous with ==(AbstractArray{Bool,N},BitArray{N}) at bitarray.jl:1062.
Make sure ==(BitArray{N},BitArray{N}) is defined first.
Warning: New definition ==(BitArray{N},AbstractArray{Bool,N}) at /usr/local/Cellar/julia/HEAD/share/julia/base/bitarray.jl:1061 is ambiguous with ==(AbstractArray{T,N},BitArray{N}) at bitarray.jl:1064.
Make sure ==(BitArray{N},BitArray{N}) is defined first.
Warning: New definition ==(AbstractArray{Bool,N},BitArray{N}) at /usr/local/Cellar/julia/HEAD/share/julia/base/bitarray.jl:1062 is ambiguous with ==(BitArray{N},AbstractArray{Bool,N}) at bitarray.jl:1061.
Make sure ==(BitArray{N},BitArray{N}) is defined first.
Warning: New definition ==(AbstractArray{Bool,N},BitArray{N}) at /usr/local/Cellar/julia/HEAD/share/julia/base/bitarray.jl:1062 is ambiguous with ==(BitArray{N},AbstractArray{T,N}) at bitarray.jl:1063.
Make sure ==(BitArray{N},BitArray{N}) is defined first.
Warning: New definition ==(BitArray{N},AbstractArray{T,N}) at /usr/local/Cellar/julia/HEAD/share/julia/base/bitarray.jl:1063 is ambiguous with ==(AbstractArray{Bool,N},BitArray{N}) at bitarray.jl:1062.
Make sure ==(BitArray{N},BitArray{N}) is defined first.
Warning: New definition ==(BitArray{N},AbstractArray{T,N}) at /usr/local/Cellar/julia/HEAD/share/julia/base/bitarray.jl:1063 is ambiguous with ==(AbstractArray{T,N},BitArray{N}) at bitarray.jl:1064.
Make sure ==(BitArray{N},BitArray{N}) is defined first.
Warning: New definition ==(AbstractArray{T,N},BitArray{N}) at /usr/local/Cellar/julia/HEAD/share/julia/base/bitarray.jl:1064 is ambiguous with ==(BitArray{N},AbstractArray{Bool,N}) at bitarray.jl:1061.
Make sure ==(BitArray{N},BitArray{N}) is defined first.
Warning: New definition ==(AbstractArray{T,N},BitArray{N}) at /usr/local/Cellar/julia/HEAD/share/julia/base/bitarray.jl:1064 is ambiguous with ==(BitArray{N},AbstractArray{T,N}) at bitarray.jl:1063.
Make sure ==(BitArray{N},BitArray{N}) is defined first.
Warning: New definition !=(BitArray{N},AbstractArray{Bool,N}) at /usr/local/Cellar/julia/HEAD/share/julia/base/bitarray.jl:1061 is ambiguous with !=(AbstractArray{Bool,N},BitArray{N}) at bitarray.jl:1062.
Make sure !=(BitArray{N},BitArray{N}) is defined first.
Warning: New definition !=(BitArray{N},AbstractArray{Bool,N}) at /usr/local/Cellar/julia/HEAD/share/julia/base/bitarray.jl:1061 is ambiguous with !=(AbstractArray{T,N},BitArray{N}) at bitarray.jl:1064.
Make sure !=(BitArray{N},BitArray{N}) is defined first.
Warning: New definition !=(AbstractArray{Bool,N},BitArray{N}) at /usr/local/Cellar/julia/HEAD/share/julia/base/bitarray.jl:1062 is ambiguous with !=(BitArray{N},AbstractArray{Bool,N}) at bitarray.jl:1061.
Make sure !=(BitArray{N},BitArray{N}) is defined first.
Warning: New definition !=(AbstractArray{Bool,N},BitArray{N}) at /usr/local/Cellar/julia/HEAD/share/julia/base/bitarray.jl:1062 is ambiguous with !=(BitArray{N},AbstractArray{T,N}) at bitarray.jl:1063.
Make sure !=(BitArray{N},BitArray{N}) is defined first.
Warning: New definition !=(BitArray{N},AbstractArray{T,N}) at /usr/local/Cellar/julia/HEAD/share/julia/base/bitarray.jl:1063 is ambiguous with !=(AbstractArray{Bool,N},BitArray{N}) at bitarray.jl:1062.
Make sure !=(BitArray{N},BitArray{N}) is defined first.
Warning: New definition !=(BitArray{N},AbstractArray{T,N}) at /usr/local/Cellar/julia/HEAD/share/julia/base/bitarray.jl:1063 is ambiguous with !=(AbstractArray{T,N},BitArray{N}) at bitarray.jl:1064.
Make sure !=(BitArray{N},BitArray{N}) is defined first.
Warning: New definition !=(AbstractArray{T,N},BitArray{N}) at /usr/local/Cellar/julia/HEAD/share/julia/base/bitarray.jl:1064 is ambiguous with !=(BitArray{N},AbstractArray{Bool,N}) at bitarray.jl:1061.
Make sure !=(BitArray{N},BitArray{N}) is defined first.
Warning: New definition !=(AbstractArray{T,N},BitArray{N}) at /usr/local/Cellar/julia/HEAD/share/julia/base/bitarray.jl:1064 is ambiguous with !=(BitArray{N},AbstractArray{T,N}) at bitarray.jl:1063.
Make sure !=(BitArray{N},BitArray{N}) is defined first.
Dimspec not defined
in load_now at util.jl:235
in require at util.jl:185
in load_now at util.jl:235
in load_now at util.jl:235
in load_now at util.jl:247
at /usr/local/Cellar/julia/HEAD/share/julia/base/bitarray.jl:1406

@staticfloat
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This looks to be an issue beyond Homebrew. Issue reported here.

@staticfloat
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This has been fixed, can you confirm? You'll need to run a require("pkg"); Pkg.update(); first.

@AlexMikhalev
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Yep homebrew issue solved. Forgot to comment after Pkg.update().

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