Installation error when Julia is built from source

[yurivish]

I tried installing Arpack on 0.7 beta and saw this error trying to run eigs:

julia> A = Diagonal(1:4);
WARNING: Base.Diagonal is deprecated: it has been moved to the standard library package `LinearAlgebra`.
Add `using LinearAlgebra` to your imports.
 in module Main

julia> λ, ϕ = eigs(A, nev = 2);
ERROR: error compiling saupd: could not load library ""
dlopen(.dylib, 1): image not found
Stacktrace:
 [1] aupd_wrapper(::Any, ::getfield(Arpack, Symbol("#matvecA!#24")){LinearAlgebra.Diagonal{Float64,Array{Float64,1}}}, ::getfield(Arpack, Symbol("##18#25")), ::getfield(Arpack, Symbol("##19#26")), ::Int64, ::Bool, ::Bool, ::String, ::Int64, ::Int64, ::String, ::Float64, ::Int64, ::Int64, ::Array{Float64,1}) at /Users/yurivish/.julia/packages/Arpack/Rkbg/src/libarpack.jl:42
 [2] #_eigs#17(::Int64, ::Int64, ::Symbol, ::Float64, ::Int64, ::Nothing, ::Array{Float64,1}, ::Bool, ::Any, ::Any, ::Any) at /Users/yurivish/.julia/packages/Arpack/Rkbg/src/Arpack.jl:176
 [3] (::getfield(Arpack, Symbol("#kw##eigs")))(::NamedTuple{(:nev,),Tuple{Int64}}, ::typeof(eigs), ::LinearAlgebra.Diagonal{Int64,UnitRange{Int64}}) at ./none:0
 [4] top-level scope at none:0

To see if this was solved on master, I tried installing it. But this happens when I try to develop Arpack#master:

Error: Error building `Arpack`:
│ [ Info: Downloading https://github.com/JuliaLinearAlgebra/ArpackBuilder/releases/download/v3.5.0-0.2.20/ArpackBuilder.x86_64-apple-darwin14.tar.gz to /Users/yurivish/.julia/dev/Arpack/deps/usr/downloads/ArpackBuilder.x86_64-apple-darwin14.tar.gz...
│ ┌ Warning: `wait(t::Task)` is deprecated, use `fetch(t)` instead.
│ │   caller = macro expansion at OutputCollector.jl:63 [inlined]
│ └ @ Core OutputCollector.jl:63
│ ┌ Warning: `wait(t::Task)` is deprecated, use `fetch(t)` instead.
│ │   caller = wait(::OutputCollector) at OutputCollector.jl:158
│ └ @ BinaryProvider OutputCollector.jl:158
│ ┌ Warning: `wait(t::Task)` is deprecated, use `fetch(t)` instead.
│ │   caller = wait(::OutputCollector) at OutputCollector.jl:159
│ └ @ BinaryProvider OutputCollector.jl:159
│ ┌ Warning: `wait(t::Task)` is deprecated, use `fetch(t)` instead.
│ │   caller = wait(::OutputCollector) at OutputCollector.jl:163
│ └ @ BinaryProvider OutputCollector.jl:163
│ ERROR: LoadError: LibraryProduct(nothing, ["libarpack"], :libarpack, "Prefix(/Users/yurivish/.julia/dev/Arpack/deps/usr)") is not satisfied, cannot generate deps.jl!
│ Stacktrace:
│  [1] error at ./error.jl:33 [inlined]
│  [2] #write_deps_file#134(::Bool, ::Function, ::String, ::Array{LibraryProduct,1}) at /Users/yurivish/.julia/packages/BinaryProvider/2Hlv/src/Products.jl:389
│  [3] write_deps_file(::String, ::Array{LibraryProduct,1}) at /Users/yurivish/.julia/packages/BinaryProvider/2Hlv/src/Products.jl:376
│  [4] top-level scope at none:0
│  [5] include at ./boot.jl:317 [inlined]
│  [6] include_relative(::Module, ::String) at ./loading.jl:1075
│  [7] include(::Module, ::String) at ./sysimg.jl:29
│  [8] include(::String) at ./client.jl:393
│  [9] top-level scope at none:0
│ in expression starting at /Users/yurivish/.julia/dev/Arpack/deps/build.jl:40

julia> versioninfo()
Julia Version 0.7.0-beta.0
Commit f41b1ecaec (2018-06-24 01:32 UTC)
Platform Info:
  OS: macOS (x86_64-apple-darwin16.7.0)
  CPU: Intel(R) Core(TM) i7-3615QM CPU @ 2.30GHz
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-6.0.0 (ORCJIT, ivybridge)
Environment:
  JULIA_EDITOR = subl

[andreasnoack]

Might be dup of #3. Did you build from source? What do you get from otool -L usr/lib/libopenblas64_.dylib?

[bicycle1885]

I encountered the same problem on macOS, 0.7.0-beta.0.

~/v/julia ((v0.7.0-beta)|…) $ otool -L usr/lib/libopenblas64_.dylib
usr/lib/libopenblas64_.dylib:
        @rpath/libopenblas64_.dylib (compatibility version 0.0.0, current version 0.0.0)
        /usr/local/opt/gcc/lib/gcc/6/libgfortran.3.dylib (compatibility version 4.0.0, current version 4.0.0)
        /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1238.60.2)
        /usr/local/opt/gcc/lib/gcc/6/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0)
        /usr/local/lib/gcc/6/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0)

Do we need to wait for the official binaries of Julia 0.7.0-beta?

[andreasnoack]

Do we need to wait for the official binaries of Julia 0.7.0-beta?

Either that or build your OpenBLAS with GCC 7.

[bicycle1885]

Thank you. I will try.

[yurivish]

@andreasnoack this was with a build from source. Thanks to the pointer to Viral's issue – I didn't see it since it was closed.

$ otool -L usr/lib/libopenblas64_.dylib
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/objdump: 'usr/lib/libopenblas64_.dylib': No such file or directory

[andreasnoack]

@yurivish You'll need to adjust the path to match the usr directory within your root Julia directory.

[blakejohnson]

$ otool -L usr/lib/libopenblas64_.dylib 
usr/lib/libopenblas64_.dylib:
	@rpath/libopenblas64_.dylib (compatibility version 0.0.0, current version 0.0.0)
	/usr/local/opt/gcc/lib/gcc/7/libgfortran.4.dylib (compatibility version 5.0.0, current version 5.0.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1238.60.2)
	/usr/local/opt/gcc/lib/gcc/7/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0)
	/usr/local/lib/gcc/7/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0)

[bicycle1885]

FYI, Julia 0.7-beta binary for macOS is now available (https://julialang.org/downloads/), which solves the problem.

[andreasnoack]

@blakejohnson Things are more wrong than first anticipated. So the system libgfortran is apparently not in the RPATH. I'm able to get it working with DYLD_LIBRARY_PATH=/usr/local/opt/gcc@7/lib/gcc/7 julia-dev which is, of course, not a real solution but it identifies the issue here. Will have to hear @staticfloat what a proper solution would look like.

[RalphAS]

Another possible workaround is to copy (or maybe hard link) libgfortran.so.4 from another Julia package (e.g. SpecialFunctions) into Arpack/XXXX/deps/usr/lib and then run pkg> build Arpack. This appears to be working for me, with Julia built from source on Linux.

[maleadt]

Just for completeness (coming from #9), this obviously also occurs on Linux when not building with GCC 7. Doesn't seem easy to work around, with eg. Arch Linux' gcc7 package not providing libgfortran.4, and Debian Stable using GCC 6 / libgfortran.3 with no means to (safely) install GCC 7.