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Failure to precompile, no libquadmath.so.0 #1922

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NOTtheMessiah opened this issue Dec 6, 2024 · 2 comments
Closed

Failure to precompile, no libquadmath.so.0 #1922

NOTtheMessiah opened this issue Dec 6, 2024 · 2 comments

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@NOTtheMessiah
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after trying to install fresh, it fails to find libquadmath.so.0:

Precompiling Distributions...
Info Given Distributions was explicitly requested, output will be shown live 
ERROR: LoadError: InitError: could not load library "~/.julia/artifacts/abf4b5086b4eb867021118c85b2cc11a15b764a9/lib/libopenspecfun.so"
libquadmath.so.0: cannot open shared object file: No such file or directory
Stacktrace:
  [1] dlopen(s::String, flags::UInt32; throw_error::Bool)
    @ Base.Libc.Libdl ./libdl.jl:120
  [2] dlopen(s::String, flags::UInt32)
    @ Base.Libc.Libdl ./libdl.jl:119
  [3] macro expansion
    @ ~/.julia/packages/JLLWrappers/jXOYx/src/products/library_generators.jl:63 [inlined]
  [4] __init__()
    @ OpenSpecFun_jll ~/.julia/packages/OpenSpecFun_jll/1Zaof/src/wrappers/x86_64-linux-gnu-libgfortran5.jl:9
  [5] run_module_init(mod::Module, i::Int64)
    @ Base ./loading.jl:1336
  [6] register_restored_modules(sv::Core.SimpleVector, pkg::Base.PkgId, path::String)
    @ Base ./loading.jl:1324
  [7] _include_from_serialized(pkg::Base.PkgId, path::String, ocachepath::String, depmods::Vector{Any}, ignore_native::Nothing; register::Bool)
    @ Base ./loading.jl:1213
  [8] _include_from_serialized (repeats 2 times)
    @ ./loading.jl:1169 [inlined]
  [9] _require_search_from_serialized(pkg::Base.PkgId, sourcepath::String, build_id::UInt128, stalecheck::Bool; reasons::Dict{String, Int64}, DEPOT_PATH::Vector{String})
    @ Base ./loading.jl:1985
 [10] _require(pkg::Base.PkgId, env::String)
    @ Base ./loading.jl:2450
 [11] __require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:2315
 [12] #invoke_in_world#3
    @ ./essentials.jl:1089 [inlined]
 [13] invoke_in_world
    @ ./essentials.jl:1086 [inlined]
 [14] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:2302
 [15] macro expansion
    @ ./loading.jl:2241 [inlined]
 [16] macro expansion
    @ ./lock.jl:273 [inlined]
 [17] __require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2198
 [18] #invoke_in_world#3
    @ ./essentials.jl:1089 [inlined]
 [19] invoke_in_world
    @ ./essentials.jl:1086 [inlined]
 [20] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2191
 [21] include
    @ ./Base.jl:557 [inlined]
 [22] 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, UInt128}}, source::String)
    @ Base ./loading.jl:2790
 [23] top-level scope
    @ stdin:5
during initialization of module OpenSpecFun_jll
in expression starting at ~/.julia/packages/SpecialFunctions/npKKV/src/SpecialFunctions.jl:1
in expression starting at stdin:5
ERROR: LoadError: Failed to precompile SpecialFunctions [276daf66-3868-5448-9aa4-cd146d93841b] to "~/.julia/compiled/v1.11/SpecialFunctions/jl_46RZHJ".
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; flags::Cmd, cacheflags::Base.CacheFlags, reasons::Dict{String, Int64}, isext::Bool)
    @ Base ./loading.jl:3085
  [3] (::Base.var"#1082#1083"{Base.PkgId})()
    @ Base ./loading.jl:2492
  [4] mkpidlock(f::Base.var"#1082#1083"{Base.PkgId}, at::String, pid::Int32; kwopts::@Kwargs{stale_age::Int64, wait::Bool})
    @ FileWatching.Pidfile /nix/store/gr0m7w6gmsan5bn1swd9bxp4ak1jxfam-julia-1.11.1/share/julia/stdlib/v1.11/FileWatching/src/pidfile.jl:95
  [5] #mkpidlock#6
    @ /nix/store/gr0m7w6gmsan5bn1swd9bxp4ak1jxfam-julia-1.11.1/share/julia/stdlib/v1.11/FileWatching/src/pidfile.jl:90 [inlined]
  [6] trymkpidlock(::Function, ::Vararg{Any}; kwargs::@Kwargs{stale_age::Int64})
    @ FileWatching.Pidfile /nix/store/gr0m7w6gmsan5bn1swd9bxp4ak1jxfam-julia-1.11.1/share/julia/stdlib/v1.11/FileWatching/src/pidfile.jl:116
  [7] #invokelatest#2
    @ ./essentials.jl:1057 [inlined]
  [8] invokelatest
    @ ./essentials.jl:1052 [inlined]
  [9] maybe_cachefile_lock(f::Base.var"#1082#1083"{Base.PkgId}, pkg::Base.PkgId, srcpath::String; stale_age::Int64)
    @ Base ./loading.jl:3609
 [10] maybe_cachefile_lock
    @ ./loading.jl:3606 [inlined]
 [11] _require(pkg::Base.PkgId, env::String)
    @ Base ./loading.jl:2488
 [12] __require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:2315
 [13] #invoke_in_world#3
    @ ./essentials.jl:1089 [inlined]
 [14] invoke_in_world
    @ ./essentials.jl:1086 [inlined]
 [15] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:2302
 [16] macro expansion
    @ ./loading.jl:2241 [inlined]
 [17] macro expansion
    @ ./lock.jl:273 [inlined]
 [18] __require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2198
 [19] #invoke_in_world#3
    @ ./essentials.jl:1089 [inlined]
 [20] invoke_in_world
    @ ./essentials.jl:1086 [inlined]
 [21] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2191
 [22] include
    @ ./Base.jl:557 [inlined]
 [23] 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, UInt128}}, source::String)
    @ Base ./loading.jl:2790
 [24] top-level scope
    @ stdin:5
in expression starting at ~/.julia/packages/StatsFuns/NSRpu/src/StatsFuns.jl:1
in expression starting at stdin:5
ERROR: LoadError: Failed to precompile StatsFuns [4c63d2b9-4356-54db-8cca-17b64c39e42c] to "~/.julia/compiled/v1.11/StatsFuns/jl_T0IbLt".
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; flags::Cmd, cacheflags::Base.CacheFlags, reasons::Dict{String, Int64}, isext::Bool)
    @ Base ./loading.jl:3085
  [3] (::Base.var"#1082#1083"{Base.PkgId})()
    @ Base ./loading.jl:2492
  [4] mkpidlock(f::Base.var"#1082#1083"{Base.PkgId}, at::String, pid::Int32; kwopts::@Kwargs{stale_age::Int64, wait::Bool})
    @ FileWatching.Pidfile /nix/store/gr0m7w6gmsan5bn1swd9bxp4ak1jxfam-julia-1.11.1/share/julia/stdlib/v1.11/FileWatching/src/pidfile.jl:95
  [5] #mkpidlock#6
    @ /nix/store/gr0m7w6gmsan5bn1swd9bxp4ak1jxfam-julia-1.11.1/share/julia/stdlib/v1.11/FileWatching/src/pidfile.jl:90 [inlined]
  [6] trymkpidlock(::Function, ::Vararg{Any}; kwargs::@Kwargs{stale_age::Int64})
    @ FileWatching.Pidfile /nix/store/gr0m7w6gmsan5bn1swd9bxp4ak1jxfam-julia-1.11.1/share/julia/stdlib/v1.11/FileWatching/src/pidfile.jl:116
  [7] #invokelatest#2
    @ ./essentials.jl:1057 [inlined]
  [8] invokelatest
    @ ./essentials.jl:1052 [inlined]
  [9] maybe_cachefile_lock(f::Base.var"#1082#1083"{Base.PkgId}, pkg::Base.PkgId, srcpath::String; stale_age::Int64)
    @ Base ./loading.jl:3609
 [10] maybe_cachefile_lock
    @ ./loading.jl:3606 [inlined]
 [11] _require(pkg::Base.PkgId, env::String)
    @ Base ./loading.jl:2488
 [12] __require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:2315
 [13] #invoke_in_world#3
    @ ./essentials.jl:1089 [inlined]
 [14] invoke_in_world
    @ ./essentials.jl:1086 [inlined]
 [15] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:2302
 [16] macro expansion
    @ ./loading.jl:2241 [inlined]
 [17] macro expansion
    @ ./lock.jl:273 [inlined]
 [18] __require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2198
 [19] #invoke_in_world#3
    @ ./essentials.jl:1089 [inlined]
 [20] invoke_in_world
    @ ./essentials.jl:1086 [inlined]
 [21] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2191
 [22] include
    @ ./Base.jl:557 [inlined]
 [23] 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, UInt128}}, source::Nothing)
    @ Base ./loading.jl:2790
 [24] top-level scope
    @ stdin:5
in expression starting at ~/.julia/packages/Distributions/Qeo2J/src/Distributions.jl:1
in expression starting at stdin:5
  ✗ SpecialFunctions
  ✗ HypergeometricFunctions
  ✗ StatsFuns
  ✗ Distributions
  0 dependencies successfully precompiled in 11 seconds. 61 already precompiled.

ERROR: The following 1 direct dependency failed to precompile:

Distributions 

Failed to precompile Distributions [31c24e10-a181-5473-b8eb-7969acd0382f] to "~/.julia/compiled/v1.11/Distributions/jl_PMLUr4".
ERROR: LoadError: InitError: could not load library "~/.julia/artifacts/abf4b5086b4eb867021118c85b2cc11a15b764a9/lib/libopenspecfun.so"
libquadmath.so.0: cannot open shared object file: No such file or directory
Stacktrace:
  [1] dlopen(s::String, flags::UInt32; throw_error::Bool)
    @ Base.Libc.Libdl ./libdl.jl:120
  [2] dlopen(s::String, flags::UInt32)
    @ Base.Libc.Libdl ./libdl.jl:119
  [3] macro expansion
    @ ~/.julia/packages/JLLWrappers/jXOYx/src/products/library_generators.jl:63 [inlined]
  [4] __init__()
    @ OpenSpecFun_jll ~/.julia/packages/OpenSpecFun_jll/1Zaof/src/wrappers/x86_64-linux-gnu-libgfortran5.jl:9
  [5] run_module_init(mod::Module, i::Int64)
    @ Base ./loading.jl:1336
  [6] register_restored_modules(sv::Core.SimpleVector, pkg::Base.PkgId, path::String)
    @ Base ./loading.jl:1324
  [7] _include_from_serialized(pkg::Base.PkgId, path::String, ocachepath::String, depmods::Vector{Any}, ignore_native::Nothing; register::Bool)
    @ Base ./loading.jl:1213
  [8] _include_from_serialized (repeats 2 times)
    @ ./loading.jl:1169 [inlined]
  [9] _require_search_from_serialized(pkg::Base.PkgId, sourcepath::String, build_id::UInt128, stalecheck::Bool; reasons::Dict{String, Int64}, DEPOT_PATH::Vector{String})
    @ Base ./loading.jl:1985
 [10] _require(pkg::Base.PkgId, env::String)
    @ Base ./loading.jl:2450
 [11] __require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:2315
 [12] #invoke_in_world#3
    @ ./essentials.jl:1089 [inlined]
 [13] invoke_in_world
    @ ./essentials.jl:1086 [inlined]
 [14] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:2302
 [15] macro expansion
    @ ./loading.jl:2241 [inlined]
 [16] macro expansion
    @ ./lock.jl:273 [inlined]
 [17] __require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2198
 [18] #invoke_in_world#3
    @ ./essentials.jl:1089 [inlined]
 [19] invoke_in_world
    @ ./essentials.jl:1086 [inlined]
 [20] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2191
 [21] include
    @ ./Base.jl:557 [inlined]
 [22] 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, UInt128}}, source::String)
    @ Base ./loading.jl:2790
 [23] top-level scope
    @ stdin:5
during initialization of module OpenSpecFun_jll
in expression starting at ~/.julia/packages/SpecialFunctions/npKKV/src/SpecialFunctions.jl:1
in expression starting at stdin:5
ERROR: LoadError: Failed to precompile SpecialFunctions [276daf66-3868-5448-9aa4-cd146d93841b] to "~/.julia/compiled/v1.11/SpecialFunctions/jl_46RZHJ".
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; flags::Cmd, cacheflags::Base.CacheFlags, reasons::Dict{String, Int64}, isext::Bool)
    @ Base ./loading.jl:3085
  [3] (::Base.var"#1082#1083"{Base.PkgId})()
    @ Base ./loading.jl:2492
  [4] mkpidlock(f::Base.var"#1082#1083"{Base.PkgId}, at::String, pid::Int32; kwopts::@Kwargs{stale_age::Int64, wait::Bool})
    @ FileWatching.Pidfile /nix/store/gr0m7w6gmsan5bn1swd9bxp4ak1jxfam-julia-1.11.1/share/julia/stdlib/v1.11/FileWatching/src/pidfile.jl:95
  [5] #mkpidlock#6
    @ /nix/store/gr0m7w6gmsan5bn1swd9bxp4ak1jxfam-julia-1.11.1/share/julia/stdlib/v1.11/FileWatching/src/pidfile.jl:90 [inlined]
  [6] trymkpidlock(::Function, ::Vararg{Any}; kwargs::@Kwargs{stale_age::Int64})
    @ FileWatching.Pidfile /nix/store/gr0m7w6gmsan5bn1swd9bxp4ak1jxfam-julia-1.11.1/share/julia/stdlib/v1.11/FileWatching/src/pidfile.jl:116
  [7] #invokelatest#2
    @ ./essentials.jl:1057 [inlined]
  [8] invokelatest
    @ ./essentials.jl:1052 [inlined]
  [9] maybe_cachefile_lock(f::Base.var"#1082#1083"{Base.PkgId}, pkg::Base.PkgId, srcpath::String; stale_age::Int64)
    @ Base ./loading.jl:3609
 [10] maybe_cachefile_lock
    @ ./loading.jl:3606 [inlined]
 [11] _require(pkg::Base.PkgId, env::String)
    @ Base ./loading.jl:2488
 [12] __require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:2315
 [13] #invoke_in_world#3
    @ ./essentials.jl:1089 [inlined]
 [14] invoke_in_world
    @ ./essentials.jl:1086 [inlined]
 [15] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:2302
 [16] macro expansion
    @ ./loading.jl:2241 [inlined]
 [17] macro expansion
    @ ./lock.jl:273 [inlined]
 [18] __require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2198
 [19] #invoke_in_world#3
    @ ./essentials.jl:1089 [inlined]
 [20] invoke_in_world
    @ ./essentials.jl:1086 [inlined]
 [21] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2191
 [22] include
    @ ./Base.jl:557 [inlined]
 [23] 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, UInt128}}, source::String)
    @ Base ./loading.jl:2790
 [24] top-level scope
    @ stdin:5
in expression starting at ~/.julia/packages/StatsFuns/NSRpu/src/StatsFuns.jl:1
in expression starting at stdin:5
ERROR: LoadError: Failed to precompile StatsFuns [4c63d2b9-4356-54db-8cca-17b64c39e42c] to "~/.julia/compiled/v1.11/StatsFuns/jl_T0IbLt".
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; flags::Cmd, cacheflags::Base.CacheFlags, reasons::Dict{String, Int64}, isext::Bool)
    @ Base ./loading.jl:3085
  [3] (::Base.var"#1082#1083"{Base.PkgId})()
    @ Base ./loading.jl:2492
  [4] mkpidlock(f::Base.var"#1082#1083"{Base.PkgId}, at::String, pid::Int32; kwopts::@Kwargs{stale_age::Int64, wait::Bool})
    @ FileWatching.Pidfile /nix/store/gr0m7w6gmsan5bn1swd9bxp4ak1jxfam-julia-1.11.1/share/julia/stdlib/v1.11/FileWatching/src/pidfile.jl:95
  [5] #mkpidlock#6
    @ /nix/store/gr0m7w6gmsan5bn1swd9bxp4ak1jxfam-julia-1.11.1/share/julia/stdlib/v1.11/FileWatching/src/pidfile.jl:90 [inlined]
  [6] trymkpidlock(::Function, ::Vararg{Any}; kwargs::@Kwargs{stale_age::Int64})
    @ FileWatching.Pidfile /nix/store/gr0m7w6gmsan5bn1swd9bxp4ak1jxfam-julia-1.11.1/share/julia/stdlib/v1.11/FileWatching/src/pidfile.jl:116
  [7] #invokelatest#2
    @ ./essentials.jl:1057 [inlined]
  [8] invokelatest
    @ ./essentials.jl:1052 [inlined]
  [9] maybe_cachefile_lock(f::Base.var"#1082#1083"{Base.PkgId}, pkg::Base.PkgId, srcpath::String; stale_age::Int64)
    @ Base ./loading.jl:3609
 [10] maybe_cachefile_lock
    @ ./loading.jl:3606 [inlined]
 [11] _require(pkg::Base.PkgId, env::String)
    @ Base ./loading.jl:2488
 [12] __require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:2315
 [13] #invoke_in_world#3
    @ ./essentials.jl:1089 [inlined]
 [14] invoke_in_world
    @ ./essentials.jl:1086 [inlined]
 [15] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:2302
 [16] macro expansion
    @ ./loading.jl:2241 [inlined]
 [17] macro expansion
    @ ./lock.jl:273 [inlined]
 [18] __require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2198
 [19] #invoke_in_world#3
    @ ./essentials.jl:1089 [inlined]
 [20] invoke_in_world
    @ ./essentials.jl:1086 [inlined]
 [21] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2191
 [22] include
    @ ./Base.jl:557 [inlined]
 [23] 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, UInt128}}, source::Nothing)
    @ Base ./loading.jl:2790
 [24] top-level scope
    @ stdin:5
in expression starting at ~/.julia/packages/Distributions/Qeo2J/src/Distributions.jl:1
in expression starting at stdin:
@devmotion
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That seems to be a problem with the installation of SpecialFunctions. I can't transfer the issue to the SpecialFunctions repo though (it's in a different Github organization), so I'll close this issue and would ask you to open a new issue there. I'd recommend including information about the Julia version, your OS, and your architecture in the issue, by posting the output of versioninfo() in the REPL as well.

@NOTtheMessiah
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I'm using Julia 1.11.1 on NixOS. Seems like libopenspecfun.so.1.4 in the Julia artifacts was missing some dynamic links to the right places, despite being include in many places (in the Julia package, in gfortran, and in libopenspec). Possibly an error with autoPatchelf, or a problem in Yggdrasil. Regardless, I was able to write a temporary workaround using patchelf to link to the files included with the Julia package itself:

sudo patchelf --replace-needed libgfortran.so.5 $(nix path-info nixpkgs#julia)/lib/julia/libgfortran.so.5 libopenspecfun.so.1.4
sudo patchelf --replace-needed libquadmath.so.0 $(nix path-info nixpkgs#julia)/lib/julia/libquadmath.so.0 libopenspecfun.so.1.4

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@devmotion @NOTtheMessiah