Cannot install RMS due to Julia update #248
Description
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