Error while installing DataFrames

Konstantin_Kuznetsov · September 12, 2023, 10:21am

Dear all,

I have an error during installation of package DataFrames or DataDeps under Ubuntu 22.04 processor AMD (and also the same error on Apple M1 pro). The error is the following one:

(@v1.9) pkg> add DataFrames
    Updating registry at `~/.julia/registries/General.toml`
   Resolving package versions...
  No Changes to `~/.julia/environments/v1.9/Project.toml`
  No Changes to `~/.julia/environments/v1.9/Manifest.toml`
Precompiling project...
  2 dependencies successfully precompiled in 10 seconds. 418 already precompiled.
  2 dependencies had warnings during precompilation:
┌ OptimizationSparseForwardDiffExt [701a54de-6e64-5ef9-9423-e7f6ffec093b]
│  ┌ Warning: Module OptimizationSparseForwardDiffExt with build ID ffffffff-ffff-ffff-0000-77c2cd8cda92 is missing from the cache.
│  │ This may mean OptimizationSparseForwardDiffExt [701a54de-6e64-5ef9-9423-e7f6ffec093b] does not support precompilation but is imported by a module that does.
│  └ @ Base loading.jl:1793
│  ┌ Error: Error during loading of extension OptimizationSparseForwardDiffExt of Optimization, use `Base.retry_load_extensions()` to retry.
│  │   exception =
│  │    1-element ExceptionStack:
│  │    Declaring __precompile__(false) is not allowed in files that are being precompiled.
│  │    Stacktrace:
│  │      [1] _require(pkg::Base.PkgId, env::Nothing)
│  │        @ Base ./loading.jl:1797
│  │      [2] _require_prelocked(uuidkey::Base.PkgId, env::Nothing)
│  │        @ Base ./loading.jl:1660
│  │      [3] _require_prelocked(uuidkey::Base.PkgId)
│  │        @ Base ./loading.jl:1658
│  │      [4] run_extension_callbacks(extid::Base.ExtensionId)
│  │        @ Base ./loading.jl:1255
│  │      [5] run_extension_callbacks(pkgid::Base.PkgId)
│  │        @ Base ./loading.jl:1290
│  │      [6] run_package_callbacks(modkey::Base.PkgId)
│  │        @ Base ./loading.jl:1124
│  │      [7] _require_prelocked(uuidkey::Base.PkgId, env::String)
│  │        @ Base ./loading.jl:1667
│  │      [8] macro expansion
│  │        @ ./loading.jl:1648 [inlined]
│  │      [9] macro expansion
│  │        @ ./lock.jl:267 [inlined]
│  │     [10] require(into::Module, mod::Symbol)
│  │        @ Base ./loading.jl:1611
│  │     [11] top-level scope
│  │        @ ~/.julia/packages/Optimization/7iJte/ext/OptimizationSparseFiniteDiffExt.jl:8
│  │     [12] include
│  │        @ ./Base.jl:457 [inlined]
│  │     [13] 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:2049
│  │     [14] top-level scope
│  │        @ stdin:3
│  │     [15] eval
│  │        @ ./boot.jl:370 [inlined]
│  │     [16] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
│  │        @ Base ./loading.jl:1903
│  │     [17] include_string
│  │        @ ./loading.jl:1913 [inlined]
│  │     [18] exec_options(opts::Base.JLOptions)
│  │        @ Base ./client.jl:305
│  │     [19] _start()
│  │        @ Base ./client.jl:522
│  └ @ Base loading.jl:1261
└
┌ OptimizationSparseFiniteDiffExt [92caba6d-e51c-553f-b336-9fb2cfdd4f0e]
│  ┌ Warning: Module OptimizationSparseFiniteDiffExt with build ID ffffffff-ffff-ffff-0000-77c2cdfdb0f7 is missing from the cache.
│  │ This may mean OptimizationSparseFiniteDiffExt [92caba6d-e51c-553f-b336-9fb2cfdd4f0e] does not support precompilation but is imported by a module that does.
│  └ @ Base loading.jl:1793
│  ┌ Error: Error during loading of extension OptimizationSparseFiniteDiffExt of Optimization, use `Base.retry_load_extensions()` to retry.
│  │   exception =
│  │    1-element ExceptionStack:
│  │    Declaring __precompile__(false) is not allowed in files that are being precompiled.
│  │    Stacktrace:
│  │      [1] _require(pkg::Base.PkgId, env::Nothing)
│  │        @ Base ./loading.jl:1797
│  │      [2] _require_prelocked(uuidkey::Base.PkgId, env::Nothing)
│  │        @ Base ./loading.jl:1660
│  │      [3] _require_prelocked(uuidkey::Base.PkgId)
│  │        @ Base ./loading.jl:1658
│  │      [4] run_extension_callbacks(extid::Base.ExtensionId)
│  │        @ Base ./loading.jl:1255
│  │      [5] run_extension_callbacks(pkgid::Base.PkgId)
│  │        @ Base ./loading.jl:1290
│  │      [6] run_package_callbacks(modkey::Base.PkgId)
│  │        @ Base ./loading.jl:1124
│  │      [7] _require_prelocked(uuidkey::Base.PkgId, env::String)
│  │        @ Base ./loading.jl:1667
│  │      [8] macro expansion
│  │        @ ./loading.jl:1648 [inlined]
│  │      [9] macro expansion
│  │        @ ./lock.jl:267 [inlined]
│  │     [10] require(into::Module, mod::Symbol)
│  │        @ Base ./loading.jl:1611
│  │     [11] top-level scope
│  │        @ ~/.julia/packages/Optimization/7iJte/ext/OptimizationSparseForwardDiffExt.jl:8
│  │     [12] include
│  │        @ ./Base.jl:457 [inlined]
│  │     [13] 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:2049
│  │     [14] top-level scope
│  │        @ stdin:3
│  │     [15] eval
│  │        @ ./boot.jl:370 [inlined]
│  │     [16] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
│  │        @ Base ./loading.jl:1903
│  │     [17] include_string
│  │        @ ./loading.jl:1913 [inlined]
│  │     [18] exec_options(opts::Base.JLOptions)
│  │        @ Base ./client.jl:305
│  │     [19] _start()
│  │        @ Base ./client.jl:522
│  └ @ Base loading.jl:1261

Thanks in advance for your help,
Konstantin

Sevi · September 13, 2023, 3:03pm

Welcome to the forum!

From the logged text it seems like DataFrames is already in your environment (because there are No Changes to the [Project/Manifest] file). And based on the errors, it looks like the culprit is related to the Optimization.jl package. So I’m not sure that it’s really DataFrames that causes the issue

Maybe these steps can help to narrow down the issue:

Can you install any other package in the environment? Or run pkg> precompile without adding any new packages?
If you create a new environment and add DataFrames, e.g. like so
```
pkg> activate --temp
pkg> add DataFrames
```
Do you get the same error?
It looks like you are using the “global” environment. Are there a lot of packages in there? Can you upgrade the packages with pkg> up (perhaps make a copy of the file ~/.julia/environments/v1.9/Manifest.toml before that, so you know which versions you have installed at the moment.

abelsiqueira · September 18, 2023, 1:10pm

I have a similar issue with different packages here.

kristoffer.carlsson · September 18, 2023, 1:30pm

There is some issue with this extension for which the root cause is still being tracked down.