Distributions and Arpack fail to build

General Usage
1

After updating my packages, I encountered a problem building/precompiling distributions and arpack. The issue seems to be Arpack. Does anyone know how to fix this?

Thanks

OS: Mac 10.11.6
Julia 1.0

julia> using Distributions
[ Info: Precompiling Distributions [31c24e10-a181-5473-b8eb-7969acd0382f]
ERROR: LoadError: No deps.jl file could be found. Please try running Pkg.build("Arpack").
Currently, the build command might fail when Julia has been built from source
and the recommendation is to use the official binaries from julialang.org.
For more info see https://github.com/JuliaLinearAlgebra/Arpack.jl/issues/5.

Stacktrace:
 [1] top-level scope at /Users/christopher.fisher/.julia/packages/Arpack/UiiMc/src/Arpack.jl:19
 [2] include at ./boot.jl:317 [inlined]
 [3] include_relative(::Module, ::String) at ./loading.jl:1038
 [4] include(::Module, ::String) at ./sysimg.jl:29
 [5] top-level scope at none:2
 [6] eval at ./boot.jl:319 [inlined]
 [7] eval(::Expr) at ./client.jl:389
 [8] top-level scope at ./none:3
in expression starting at /Users/christopher.fisher/.julia/packages/Arpack/UiiMc/src/Arpack.jl:16
ERROR: LoadError: LoadError: Failed to precompile Arpack [7d9fca2a-8960-54d3-9f78-7d1dccf2cb97] to /Users/christopher.fisher/.julia/compiled/v1.0/Arpack/X5VZL.ji.
Stacktrace:
 [1] error(::String) at ./error.jl:33
 [2] macro expansion at ./logging.jl:313 [inlined]
 [3] compilecache(::Base.PkgId, ::String) at ./loading.jl:1184
 [4] _require(::Base.PkgId) at ./logging.jl:311
 [5] require(::Base.PkgId) at ./loading.jl:852
 [6] macro expansion at ./logging.jl:311 [inlined]
 [7] require(::Module, ::Symbol) at ./loading.jl:834
 [8] include at ./boot.jl:317 [inlined]
 [9] include_relative(::Module, ::String) at ./loading.jl:1038
 [10] include at ./sysimg.jl:29 [inlined]
 [11] include(::String) at /Users/christopher.fisher/.julia/packages/PDMats/mL7bX/src/PDMats.jl:3
 [12] top-level scope at /Users/christopher.fisher/.julia/packages/PDMats/mL7bX/src/PDMats.jl:53
 [13] include at ./boot.jl:317 [inlined]
 [14] include_relative(::Module, ::String) at ./loading.jl:1038
 [15] include(::Module, ::String) at ./sysimg.jl:29
 [16] top-level scope at none:2
 [17] eval at ./boot.jl:319 [inlined]
 [18] eval(::Expr) at ./client.jl:389
 [19] top-level scope at ./none:3
in expression starting at /Users/christopher.fisher/.julia/packages/PDMats/mL7bX/src/pdsparsemat.jl:1
in expression starting at /Users/christopher.fisher/.julia/packages/PDMats/mL7bX/src/PDMats.jl:52
ERROR: LoadError: Failed to precompile PDMats [90014a1f-27ba-587c-ab20-58faa44d9150] to /Users/christopher.fisher/.julia/compiled/v1.0/PDMats/wuzEE.ji.
Stacktrace:
 [1] error(::String) at ./error.jl:33
 [2] macro expansion at ./logging.jl:313 [inlined]
 [3] compilecache(::Base.PkgId, ::String) at ./loading.jl:1184
 [4] _require(::Base.PkgId) at ./logging.jl:311
 [5] require(::Base.PkgId) at ./loading.jl:852
 [6] macro expansion at ./logging.jl:311 [inlined]
 [7] require(::Module, ::Symbol) at ./loading.jl:834
 [8] include at ./boot.jl:317 [inlined]
 [9] include_relative(::Module, ::String) at ./loading.jl:1038
 [10] include(::Module, ::String) at ./sysimg.jl:29
 [11] top-level scope at none:2
 [12] eval at ./boot.jl:319 [inlined]
 [13] eval(::Expr) at ./client.jl:389
 [14] top-level scope at ./none:3
in expression starting at /Users/christopher.fisher/.julia/packages/Distributions/WHjOk/src/Distributions.jl:3
ERROR: Failed to precompile Distributions [31c24e10-a181-5473-b8eb-7969acd0382f] to /Users/christopher.fisher/.julia/compiled/v1.0/Distributions/xILW0.ji.
Stacktrace:
 [1] macro expansion at ./logging.jl:313 [inlined]
 [2] compilecache(::Base.PkgId, ::String) at ./loading.jl:1184
 [3] macro expansion at ./logging.jl:311 [inlined]
 [4] _require(::Base.PkgId) at ./loading.jl:941
 [5] require(::Base.PkgId) at ./loading.jl:852
 [6] macro expansion at ./logging.jl:311 [inlined]
 [7] require(::Module, ::Symbol) at ./loading.jl:834

(v1.0) pkg> build Arpack
  Building Arpack → `~/.julia/packages/Arpack/UiiMc/deps/build.log`
┌ Error: Error building `Arpack`:
│ ERROR: LoadError: ArgumentError: Package Compat not found in current path:
│ - Run `Pkg.add("Compat")` to install the Compat package.
│
│ Stacktrace:
│  [1] require(::Module, ::Symbol) at ./loading.jl:817
│  [2] include at ./boot.jl:317 [inlined]
│  [3] include_relative(::Module, ::String) at ./loading.jl:1038
│  [4] include at ./sysimg.jl:29 [inlined]
│  [5] include_ifexists at ./client.jl:191 [inlined]
│  [6] load_julia_startup() at ./client.jl:288
│  [7] exec_options(::Base.JLOptions) at ./logging.jl:312
│  [8] _start() at ./client.jl:421
│ in expression starting at /Users/christopher.fisher/.julia/config/startup.jl:3
└ @ Pkg.Operations /Users/osx/buildbot/slave/package_osx64/build/usr/share/julia/stdlib/v1.0/Pkg/src/Operations.jl:1068

(v1.0) pkg> add Compat
 Resolving package versions...
  Updating `~/.julia/environments/v1.0/Project.toml`
 [no changes]
  Updating `~/.julia/environments/v1.0/Manifest.toml`
 [no changes]

(v1.0) pkg> build Arpack
  Building Arpack → `~/.julia/packages/Arpack/UiiMc/deps/build.log`
┌ Error: Error building `Arpack`:
│ ERROR: LoadError: ArgumentError: Package Compat not found in current path:
│ - Run `Pkg.add("Compat")` to install the Compat package.
│
│ Stacktrace:
│  [1] require(::Module, ::Symbol) at ./loading.jl:817
│  [2] include at ./boot.jl:317 [inlined]
│  [3] include_relative(::Module, ::String) at ./loading.jl:1038
│  [4] include at ./sysimg.jl:29 [inlined]
│  [5] include_ifexists at ./client.jl:191 [inlined]
│  [6] load_julia_startup() at ./client.jl:288
│  [7] exec_options(::Base.JLOptions) at ./logging.jl:312
│  [8] _start() at ./client.jl:421
│ in expression starting at /Users/christopher.fisher/.julia/config/startup.jl:3
└ @ Pkg.Operations /Users/osx/buildbot/slave/package_osx64/build/usr/share/julia/stdlib/v1.0/Pkg/src/Operations.jl:1068

(v1.0) pkg> st
    Status `~/.julia/environments/v1.0/Project.toml`
  [7d9fca2a] Arpack v0.3.0
  [c52e3926] Atom v0.7.8
  [6e4b80f9] BenchmarkTools v0.4.1
  [336ed68f] CSV v0.4.1
  [593b3428] CmdStan v4.3.0
  [35d6a980] ColorSchemes v2.0.0
  [34da2185] Compat v1.3.0
  [a93c6f00] DataFrames v0.14.1
  [0c46a032] DifferentialEquations v5.3.1
  [31c24e10] Distributions v0.16.4
  [7a1cc6ca] FFTW v0.2.4
  [38e38edf] GLM v1.0.1
  [a98d9a8b] Interpolations v0.10.3
  [682c06a0] JSON v0.19.0
  [e5e0dc1b] Juno v0.5.3
  [b964fa9f] LaTeXStrings v1.0.3
  [984bce1d] LambertW v0.4.3
  [1671dc4f] MCMCChain v0.2.2
  [6e857e4b] MCMCDiagnostics v0.3.0
  [429524aa] Optim v0.17.1
  [91a5bcdd] Plots v0.20.6
  [438e738f] PyCall v1.18.5
  [d330b81b] PyPlot v2.6.3
  [1fd47b50] QuadGK v2.0.2
  [6f49c342] RCall v0.12.1
  [e6cf234a] RandomNumbers v1.0.2
  [295af30f] Revise v0.7.12
  [80e77ffc] StanDataFrames v0.3.0
  [8f1571ae] StanMCMCChain v0.3.0
  [60ddc479] StatPlots v0.8.1
  [2913bbd2] StatsBase v0.25.0

(v1.0) pkg>```
1 Like
2

My best bet is that you are using Julia v1.0.0 and have using Compat in your startup.jl file. Julia v1.0.0 does not have don't use startup.jl when precompiling, building and testing by fredrikekre · Pull Request #470 · JuliaLang/Pkg.jl · GitHub included. If this is the case you can either (i) upgrade to Julia v1.0.1 (which is recommended anyway) or (ii) start Julia with --startup-file=no and then pkg> build Arpack again.

3

Hi Chris,

On Julia 1.0.1, a separate ()in Pkg mode) build Arpack solved the problem for me. Julia 1.1 does not build Arpack right now.

Best,
Rob

4

Thank you Rob and fredrikere. Upgrading to Julia 1.0.1 fixed the issue.

5

Hi, @fredrikekre, I thought that maybe the new v"1.0.2" might have fixed it, but that doesn’t seem to be the case. Any other ideas?

[yakir@yakir-thinkpad ~]$ julia --startup-file=no
               _
   _       _ _(_)_     |  Documentation: https://docs.julialang.org
  (_)     | (_) (_)    |
   _ _   _| |_  __ _   |  Type "?" for help, "]?" for Pkg help.
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 1.0.2 (2018-11-08)
 _/ |\__'_|_|_|\__'_|  |  
|__/                   |

(v1.0) pkg> build Arpack
  Building Arpack → `~/.julia/packages/Arpack/UiiMc/deps/build.log`
┌ Error: Error building `Arpack`: 
│ ERROR: LoadError: LibraryProduct(nothing, ["libarpack"], :libarpack, "Prefix(/home/yakir/.julia/packages/Arpack/UiiMc/deps/usr)") is not satisfied, cannot generate deps.jl!
│ Stacktrace:
│  [1] #write_deps_file#152(::Bool, ::Function, ::String, ::Array{LibraryProduct,1}) at /home/yakir/.julia/packages/BinaryProvider/1nGWd/src/Products.jl:408
│  [2] (::getfield(BinaryProvider, Symbol("#kw##write_deps_file")))(::NamedTuple{(:verbose,),Tuple{Bool}}, ::typeof(write_deps_file), ::String, ::Array{LibraryProduct,1}) at ./none:0
│  [3] top-level scope at none:0
│  [4] include(::String) at ./client.jl:392
│  [5] top-level scope at none:0
│ in expression starting at /home/yakir/.julia/packages/Arpack/UiiMc/deps/build.jl:74
└ @ Pkg.Operations /build/julia/src/julia/usr/share/julia/stdlib/v1.0/Pkg/src/Operations.jl:1097

Thanks in advance!

6

@yakir12 Is this a self-compiled julia? Maybe you’re hitting https://github.com/JuliaLinearAlgebra/Arpack.jl/issues/5 ?

1 Like
7

Nope, I’m on Manjaro and updated today.

8

Actually, this did fix it, so you were right! Thanks!!!

1 Like
9

Thanks for this! I was bonking my head against the problem all morning. On Debian you should do:

sudo ln -s /usr/lib/x86_64-linux-gnu/libopenblas.so.0 /usr/lib/x86_64-linux-gnu/libopenblas64_.so.0
3 Likes
10

Have anyone solved this issue in Fedora or centos?

11

Thank you. So much.

12

@Yifan_Liu Maybe it’s too late but for anyone else looking for this:

Fedora 30:

ln -s /usr/lib64/libopenblas.so.0 /usr/lib64/libopenblas64_.so.0

13

Thanks a lot! Helped on Chromebook Debian Buster (Julia 1.0.3), too.