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Cannot install RMS due to Julia update #248

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calvinp0 opened this issue Feb 6, 2024 · 0 comments
Open

Cannot install RMS due to Julia update #248

calvinp0 opened this issue Feb 6, 2024 · 0 comments

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@calvinp0
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calvinp0 commented Feb 6, 2024

Julia has been updated to 1.10.0 as of yesterday (2024/02/05). Since then, RMS fails to install. I get the reported error:

┌ FiniteDiff → FiniteDiffStaticArraysExt
│  ┌ Warning: CHOLMOD version incompatibility
│  │ 
│  │ Julia was compiled with CHOLMOD version 4.0.4. It is
│  │ currently linked with version 3.0.14.
│  │ This might cause Julia to terminate when working with
│  │ sparse matrix factorizations, e.g. solving systems of
│  │ equations with \.
│  │ 
│  │ It is recommended that you use Julia with the same major
│  │ version of CHOLMOD as the one used during the build, or
│  │ download the generic binaries from www.julialang.org,
│  │ which ship with the correct versions of all dependencies.
│  └ @ SparseArrays.CHOLMOD ~/mambaforge/envs/rmg_t/share/julia/stdlib/v1.10/SparseArrays/src/solvers/cholmod.jl:206
└  
┌ ImageMetadata
│  ┌ Warning: CHOLMOD version incompatibility
│  │ 
│  │ Julia was compiled with CHOLMOD version 4.0.4. It is
│  │ currently linked with version 3.0.14.
│  │ This might cause Julia to terminate when working with
│  │ sparse matrix factorizations, e.g. solving systems of
│  │ equations with \.
│  │ 
│  │ It is recommended that you use Julia with the same major
│  │ version of CHOLMOD as the one used during the build, or
│  │ download the generic binaries from www.julialang.org,
│  │ which ship with the correct versions of all dependencies.
│  └ @ SparseArrays.CHOLMOD ~/mambaforge/envs/rmg_t/share/julia/stdlib/v1.10/SparseArrays/src/solvers/cholmod.jl:206
└  
┌ PreallocationTools → PreallocationToolsReverseDiffExt
│  ┌ Warning: CHOLMOD version incompatibility
│  │ 
│  │ Julia was compiled with CHOLMOD version 4.0.4. It is
│  │ currently linked with version 3.0.14.
│  │ This might cause Julia to terminate when working with
│  │ sparse matrix factorizations, e.g. solving systems of
│  │ equations with \.
│  │ 
│  │ It is recommended that you use Julia with the same major
│  │ version of CHOLMOD as the one used during the build, or
│  │ download the generic binaries from www.julialang.org,
│  │ which ship with the correct versions of all dependencies.
│  └ @ SparseArrays.CHOLMOD ~/mambaforge/envs/rmg_t/share/julia/stdlib/v1.10/SparseArrays/src/solvers/cholmod.jl:206
└  

The following 1 direct dependency failed to precompile:

ReactionMechanismSimulator [c2d78dd2-25c4-5b79-bebc-be6c69dd440f]

Failed to precompile ReactionMechanismSimulator [c2d78dd2-25c4-5b79-bebc-be6c69dd440f] to "/home/calvin/mambaforge/envs/rmg_t/share/julia/compiled/v1.10/ReactionMechanismSimulator/jl_wjejvK".
ERROR: LoadError: Creating a new global in closed module `__toplevel__` (`Logging`) breaks incremental compilation because the side effects will not be permanent.
Stacktrace:
 [1] include
   @ Base ./Base.jl:495 [inlined]
 [2] 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:2216
 [3] top-level scope
   @ stdin:3
in expression starting at /home/calvin/mambaforge/envs/rmg_t/share/julia/packages/ReactionMechanismSimulator/LUTup/src/ReactionMechanismSimulator.jl:1
in expression starting at stdin:ERROR: LoadError: Creating a new global in closed module `__toplevel__` (`Logging`) breaks incremental compilation because the side effects will not be permanent.
Stacktrace:
 [1] include
   @ Base ./Base.jl:495 [inlined]
 [2] 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:2216
 [3] top-level scope
   @ stdin:3
in expression starting at /home/calvin/mambaforge/envs/rmg_t/share/julia/packages/ReactionMechanismSimulator/LUTup/src/ReactionMechanismSimulator.jl:1
in expression starting at stdin:3
ERROR: Failed to precompile ReactionMechanismSimulator [c2d78dd2-25c4-5b79-bebc-be6c69dd440f] to "/home/calvin/mambaforge/envs/rmg_t/share/julia/compiled/v1.10/ReactionMechanismSimulator/jl_4MpOVk".
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)
    @ Base ./loading.jl:2462
  [3] compilecache
    @ Base ./loading.jl:2334 [inlined]
  [4] (::Base.var"#968#969"{Base.PkgId})()
    @ Base ./loading.jl:1968
  [5] mkpidlock(f::Base.var"#968#969"{Base.PkgId}, at::String, pid::Int32; kwopts::@Kwargs{stale_age::Int64, wait::Bool})
    @ FileWatching.Pidfile ~/mambaforge/envs/rmg_t/share/julia/stdlib/v1.10/FileWatching/src/pidfile.jl:93
  [6] #mkpidlock#6
    @ FileWatching.Pidfile ~/mambaforge/envs/rmg_t/share/julia/stdlib/v1.10/FileWatching/src/pidfile.jl:88 [inlined]
  [7] trymkpidlock(::Function, ::Vararg{Any}; kwargs::@Kwargs{stale_age::Int64})
    @ FileWatching.Pidfile ~/mambaforge/envs/rmg_t/share/julia/stdlib/v1.10/FileWatching/src/pidfile.jl:111
  [8] #invokelatest#2
    @ Base ./essentials.jl:889 [inlined]
  [9] invokelatest
    @ Base ./essentials.jl:884 [inlined]
 [10] maybe_cachefile_lock(f::Base.var"#968#969"{Base.PkgId}, pkg::Base.PkgId, srcpath::String; stale_age::Int64)
    @ Base ./loading.jl:2977
 [11] maybe_cachefile_lock
    @ Base ./loading.jl:2974 [inlined]
 [12] _require(pkg::Base.PkgId, env::String)
    @ Base ./loading.jl:1964
 [13] __require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:1806
 [14] #invoke_in_world#3
    @ Base ./essentials.jl:921 [inlined]
 [15] invoke_in_world
    @ Base ./essentials.jl:918 [inlined]
 [16] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:1797
 [17] macro expansion
    @ Base ./loading.jl:1784 [inlined]
 [18] macro expansion
    @ Base ./lock.jl:267 [inlined]
 [19] __require(into::Module, mod::Symbol)
    @ Base ./loading.jl:1747
 [20] #invoke_in_world#3
    @ Base ./essentials.jl:921 [inlined]
 [21] invoke_in_world
    @ Base ./essentials.jl:918 [inlined]
 [22] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:1740
 [23] top-level scope
    @ none:1
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