Build Rmath takes forever

[baggepinnen]

I seem to have issues building Rmath. After having waited several minutes after the output INFO: Building Rmath and interrupting the process, I get the following stack trace. Is this supposed to take several minutes or is something wrong?

julia> Pkg.add("Rmath")
INFO: Installing Rmath v0.2.0
INFO: Building Rmath
^CERROR (unhandled task failure): InterruptException:
Stacktrace:
 [1] process_events at ./libuv.jl:82 [inlined]
 [2] wait() at ./event.jl:216
 [3] wait(::Condition) at ./event.jl:27
 [4] stream_wait(::Timer, ::Condition, ::Vararg{Condition,N} where N) at ./stream.jl:42
 [5] wait(::Timer) at ./event.jl:357
 [6] (::Base.##300#301{PyCall.##7#8{PyCall.PyObject},Timer})() at ./event.jl:430
ERROR: InterruptException:
Stacktrace:
 [1] try_yieldto(::Base.##296#297{Task}, ::Task) at ./event.jl:189
 [2] wait() at ./event.jl:234
 [3] wait(::Condition) at ./event.jl:27
 [4] wait(::Task) at ./task.jl:181
 [5] sync_end() at ./task.jl:274
 [6] macro expansion at ./task.jl:303 [inlined]
 [7] add(::String, ::Base.Pkg.Types.VersionSet) at ./pkg/entry.jl:51
 [8] (::Base.Pkg.Dir.##4#7{Array{Any,1},Base.Pkg.Entry.#add,Tuple{String}})() at ./pkg/dir.jl:36
 [9] cd(::Base.Pkg.Dir.##4#7{Array{Any,1},Base.Pkg.Entry.#add,Tuple{String}}, ::String) at ./file.jl:70
 [10] #cd#1(::Array{Any,1}, ::Function, ::Function, ::String, ::Vararg{String,N} where N) at ./pkg/dir.jl:36
 [11] add(::String) at ./pkg/pkg.jl:117

julia> versioninfo()
Julia Version 0.6.0
Commit 9036443 (2017-06-19 13:05 UTC)
Platform Info:
  OS: Linux (x86_64-pc-linux-gnu)
  CPU: Intel(R) Core(TM) i7-4790 CPU @ 3.60GHz
  WORD_SIZE: 64
  BLAS: libopenblas (USE64BITINT DYNAMIC_ARCH NO_AFFINITY Haswell)
  LAPACK: libopenblas64_
  LIBM: libopenlibm
  LLVM: libLLVM-3.9.1 (ORCJIT, haswell)

julia> Pkg.status("Rmath")
 - Rmath                         0.2.0

[simonbyrne]

Could you try:

cd(joinpath(Pkg.dir("Rmath"),"deps"))
include("build.jl")

[baggepinnen]

No luck, it's the line libRmath = library_dependency("libRmathjulia", aliases=["libRmath-julia"], validate = validate_Rmath) that stalls, if that helps

[simonbyrne]

Can you post the stack trace from when you cancelled it?

[baggepinnen]

It's the stacktrace from the first post, I cancel it at the line ^CERROR (unhandled task failure): InterruptException:

julia> include("build.jl")
^CERROR: LoadError: InterruptException:
Stacktrace:
 [1] process_events at ./libuv.jl:82 [inlined]
 [2] wait() at ./event.jl:216
 [3] wait(::Condition) at ./event.jl:27
 [4] stream_wait(::Base.PipeEndpoint, ::Condition, ::Vararg{Condition,N} where N) at ./stream.jl:42
 [5] close(::Base.PipeEndpoint) at ./stream.jl:326
 [6] #eachline#379(::Bool, ::Function, ::Cmd, ::Base.DevNullStream) at ./process.jl:556
 [7] (::Base.#kw##eachline)(::Array{Any,1}, ::Base.#eachline, ::Cmd, ::Base.DevNullStream) at ./<missing>:0
 [8] read_sonames() at /local/home/fredrikb/.julia/v0.6/BinDeps/src/dependencies.jl:382
 [9] lookup_soname(::String) at /local/home/fredrikb/.julia/v0.6/BinDeps/src/dependencies.jl:415
 [10] #_find_library#46(::Type{T} where T, ::Function, ::BinDeps.LibraryDependency) at /local/home/fredrikb/.julia/v0.6/BinDeps/src/dependencies.jl:683
 [11] satisfy!(::BinDeps.LibraryDependency, ::Array{DataType,1}) at /local/home/fredrikb/.julia/v0.6/BinDeps/src/dependencies.jl:895 (repeats 2 times)
 [12] macro expansion at /local/home/fredrikb/.julia/v0.6/BinDeps/src/dependencies.jl:950 [inlined]
 [13] anonymous at ./<missing>:?
 [14] include_from_node1(::String) at ./loading.jl:569
 [15] include(::String) at ./sysimg.jl:14
while loading /local/home/fredrikb/.julia/v0.6/Rmath/deps/build.jl, in expression starting on line 42

[simonbyrne]

@tkelman Any ideas?

[tkelman]

Try Pkg.pin("BinDeps", v"0.6.0"). If that works, we revert https://github.com/JuliaLang/BinDeps.jl/pull/277 and close the corresponding base PR that's proposing to delete the old code that didn't freeze, unless Jameson can fix the new code.

[baggepinnen]

That did the trick!

julia> Pkg.pin("BinDeps", v"0.6.0")
INFO: Creating BinDeps branch pinned.264e0860.tmp
INFO: No packages to install, update or remove

julia> Pkg.build("Rmath")
WARNING: No working GUI backend found for matplotlib
INFO: Building Rmath

julia> 

Thanks a lot, this has been bugging me for a while!

[vtjnash]

@tkelman This is a bug in Julia. Please don't revert an unrelated bugfix in reaction. Will https://github.com/JuliaLang/julia/pull/22886 be backported soon? I believe that should fix the issue.

[tkelman]

BinDeps 0.7.0 should then have a minimum version requirement of julia 0.6.1

[tkelman]

given the old code works on released versions of julia and the new code doesn't, it should still be reverted for those versions of julia subject to the bug

[simonbyrne]

This should be fixed now: please reopen if not fixed by Pkg.update().