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Error missing source file while precompiling on 1.10.2 #53623

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ufechner7 opened this issue Mar 6, 2024 · 10 comments
Open

Error missing source file while precompiling on 1.10.2 #53623

ufechner7 opened this issue Mar 6, 2024 · 10 comments
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bug Indicates an unexpected problem or unintended behavior compiler:precompilation Precompilation of modules

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@ufechner7
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ufechner7 commented Mar 6, 2024 •
edited
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Using Julia on Ubuntu 22.04, installed with juliaup.

The following fails with Julia 1.10.2, but works with julia 1.10.1:

git clone https://github.com/ufechner7/KiteUtils.jl
cd KiteUtils.jl
git checkout v0.4.8
julia --project

gives the following error on 1.10.2:

ulia> using KiteUtils
    Updating registry at `~/.julia/registries/General.toml`
    Updating `~/repos/KiteUtils.jl/Project.toml`
  [69666777] + Arrow v2.7.1
  [336ed68f] + CSV v0.10.13
  [ffbed154] + DocStringExtensions v0.9.3
  [d96e819e] + Parameters v0.12.3
⌃ [731186ca] + RecursiveArrayTools v2.38.10
  [6038ab10] + Rotations v1.7.0
⌅ [90137ffa] + StaticArrays v1.5.12
  [09ab397b] + StructArrays v0.6.18
  [856f2bd8] + StructTypes v1.10.0
  [1e6cf692] + TestEnv v1.101.1
  [ddb6d928] + YAML v0.4.9
    Updating `~/repos/KiteUtils.jl/Manifest.toml`
⌅ [79e6a3ab] + Adapt v3.7.2
⌃ [4fba245c] + ArrayInterface v7.7.1
  [69666777] + Arrow v2.7.1
  [31f734f8] + ArrowTypes v2.3.0
  [c3b6d118] + BitIntegers v0.3.1
  [336ed68f] + CSV v0.10.13
  [5ba52731] + CodecLz4 v0.4.3
  [944b1d66] + CodecZlib v0.7.4
  [6b39b394] + CodecZstd v0.8.2
  [34da2185] + Compat v4.14.0
  [f0e56b4a] + ConcurrentUtilities v2.3.1
  [187b0558] + ConstructionBase v1.5.4
  [9a962f9c] + DataAPI v1.16.0
  [e2d170a0] + DataValueInterfaces v1.0.0
  [ffbed154] + DocStringExtensions v0.9.3
  [4e289a0a] + EnumX v1.0.4
  [e2ba6199] + ExprTools v0.1.10
  [48062228] + FilePathsBase v0.9.21
⌃ [46192b85] + GPUArraysCore v0.1.5
  [842dd82b] + InlineStrings v1.4.0
  [82899510] + IteratorInterfaceExtensions v1.0.0
  [692b3bcd] + JLLWrappers v1.5.0
  [e6f89c97] + LoggingExtras v1.0.3
  [78c3b35d] + Mocking v0.7.7
  [bac558e1] + OrderedCollections v1.6.3
  [d96e819e] + Parameters v0.12.3
  [69de0a69] + Parsers v2.8.1
  [2dfb63ee] + PooledArrays v1.4.3
  [aea7be01] + PrecompileTools v1.2.0
  [21216c6a] + Preferences v1.4.3
  [94ee1d12] + Quaternions v0.7.6
  [c1ae055f] + RealDot v0.1.0
  [3cdcf5f2] + RecipesBase v1.3.4
⌃ [731186ca] + RecursiveArrayTools v2.38.10
  [ae029012] + Requires v1.3.0
  [6038ab10] + Rotations v1.7.0
  [6c6a2e73] + Scratch v1.2.1
  [91c51154] + SentinelArrays v1.4.1
⌅ [90137ffa] + StaticArrays v1.5.12
  [1e83bf80] + StaticArraysCore v1.4.2
  [69024149] + StringEncodings v0.3.7
  [09ab397b] + StructArrays v0.6.18
  [856f2bd8] + StructTypes v1.10.0
⌅ [2efcf032] + SymbolicIndexingInterface v0.2.2
  [dc5dba14] + TZJData v1.1.0+2023d
  [3783bdb8] + TableTraits v1.0.1
  [bd369af6] + Tables v1.11.1
  [1e6cf692] + TestEnv v1.101.1
  [f269a46b] + TimeZones v1.13.0
  [3bb67fe8] + TranscodingStreams v0.10.4
  [3a884ed6] + UnPack v1.0.2
  [ea10d353] + WeakRefStrings v1.4.2
  [76eceee3] + WorkerUtilities v1.6.1
  [ddb6d928] + YAML v0.4.9
  [94ce4f54] + Libiconv_jll v1.17.0+0
  [5ced341a] + Lz4_jll v1.9.4+0
  [3161d3a3] + Zstd_jll v1.5.5+0
  [0dad84c5] + ArgTools v1.1.1
  [56f22d72] + Artifacts
  [2a0f44e3] + Base64
  [ade2ca70] + Dates
  [f43a241f] + Downloads v1.6.0
  [7b1f6079] + FileWatching
  [9fa8497b] + Future
  [b77e0a4c] + InteractiveUtils
  [4af54fe1] + LazyArtifacts
  [b27032c2] + LibCURL v0.6.4
  [76f85450] + LibGit2
  [8f399da3] + Libdl
  [37e2e46d] + LinearAlgebra
  [56ddb016] + Logging
  [d6f4376e] + Markdown
  [a63ad114] + Mmap
  [ca575930] + NetworkOptions v1.2.0
  [44cfe95a] + Pkg v1.10.0
  [de0858da] + Printf
  [3fa0cd96] + REPL
  [9a3f8284] + Random
  [ea8e919c] + SHA v0.7.0
  [9e88b42a] + Serialization
  [6462fe0b] + Sockets
  [2f01184e] + SparseArrays v1.10.0
  [10745b16] + Statistics v1.10.0
  [4607b0f0] + SuiteSparse
  [fa267f1f] + TOML v1.0.3
  [a4e569a6] + Tar v1.10.0
  [8dfed614] + Test
  [cf7118a7] + UUIDs
  [4ec0a83e] + Unicode
  [e66e0078] + CompilerSupportLibraries_jll v1.1.0+0
  [deac9b47] + LibCURL_jll v8.4.0+0
  [e37daf67] + LibGit2_jll v1.6.4+0
  [29816b5a] + LibSSH2_jll v1.11.0+1
  [c8ffd9c3] + MbedTLS_jll v2.28.2+1
  [14a3606d] + MozillaCACerts_jll v2023.1.10
  [4536629a] + OpenBLAS_jll v0.3.23+4
  [bea87d4a] + SuiteSparse_jll v7.2.1+1
  [83775a58] + Zlib_jll v1.2.13+1
  [8e850b90] + libblastrampoline_jll v5.8.0+1
  [8e850ede] + nghttp2_jll v1.52.0+1
  [3f19e933] + p7zip_jll v17.4.0+2
        Info Packages marked with ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. To see why use `status --outdated -m`
Precompiling KiteUtils
  1 dependency successfully precompiled in 3 seconds. 37 already precompiled.

ERROR: The following 7 direct dependencies failed to precompile:

RecursiveArrayTools [731186ca-8d62-57ce-b412-fbd966d074cd]

Error: Missing source file for RecursiveArrayTools [731186ca-8d62-57ce-b412-fbd966d074cd]
Rotations [6038ab10-8711-5258-84ad-4b1120ba62dc]

Error: Missing source file for Rotations [6038ab10-8711-5258-84ad-4b1120ba62dc]

StructArrays [09ab397b-f2b6-538f-b94a-2f83cf4a842a]

Error: Missing source file for StructArrays [09ab397b-f2b6-538f-b94a-2f83cf4a842a]

YAML [ddb6d928-2868-570f-bddf-ab3f9cf99eb6]

Error: Missing source file for YAML [ddb6d928-2868-570f-bddf-ab3f9cf99eb6]

Parameters [d96e819e-fc66-5662-9728-84c9c7592b0a]

Error: Missing source file for Parameters [d96e819e-fc66-5662-9728-84c9c7592b0a]

StructTypes [856f2bd8-1eba-4b0a-8007-ebc267875bd4]

Error: Missing source file for StructTypes [856f2bd8-1eba-4b0a-8007-ebc267875bd4]

Arrow [69666777-d1a9-59fb-9406-91d4454c9d45]

Error: Missing source file for Arrow [69666777-d1a9-59fb-9406-91d4454c9d45]
Stacktrace:
  [1] pkgerror(msg::String)
    @ Pkg.Types ~/.julia/juliaup/julia-1.10.2+0.x64.linux.gnu/share/julia/stdlib/v1.10/Pkg/src/Types.jl:70
  [2] precompile(ctx::Pkg.Types.Context, pkgs::Vector{…}; internal_call::Bool, strict::Bool, warn_loaded::Bool, already_instantiated::Bool, timing::Bool, _from_loading::Bool, kwargs::@Kwargs{…})
    @ Pkg.API ~/.julia/juliaup/julia-1.10.2+0.x64.linux.gnu/share/julia/stdlib/v1.10/Pkg/src/API.jl:1659
  [3] precompile(pkgs::Vector{Pkg.Types.PackageSpec}; io::Base.TTY, kwargs::@Kwargs{_from_loading::Bool})
    @ Pkg.API ~/.julia/juliaup/julia-1.10.2+0.x64.linux.gnu/share/julia/stdlib/v1.10/Pkg/src/API.jl:159
  [4] precompile
    @ ~/.julia/juliaup/julia-1.10.2+0.x64.linux.gnu/share/julia/stdlib/v1.10/Pkg/src/API.jl:147 [inlined]
  [5] #precompile#114
    @ ~/.julia/juliaup/julia-1.10.2+0.x64.linux.gnu/share/julia/stdlib/v1.10/Pkg/src/API.jl:146 [inlined]
  [6] #invokelatest#2
    @ ./essentials.jl:894 [inlined]
  [7] invokelatest
    @ ./essentials.jl:889 [inlined]
  [8] _require(pkg::Base.PkgId, env::String)
    @ Base ./loading.jl:1963
  [9] __require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:1812
 [10] #invoke_in_world#3
    @ ./essentials.jl:926 [inlined]
 [11] invoke_in_world
    @ ./essentials.jl:923 [inlined]
 [12] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:1803
 [13] macro expansion
    @ ./loading.jl:1790 [inlined]
 [14] macro expansion
    @ ./lock.jl:267 [inlined]
 [15] __require(into::Module, mod::Symbol)
    @ Base ./loading.jl:1753
 [16] #invoke_in_world#3
    @ ./essentials.jl:926 [inlined]
 [17] invoke_in_world
    @ ./essentials.jl:923 [inlined]
 [18] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:1746
Some type information was truncated. Use `show(err)` to see complete types.

Versioninfo:

julia> versioninfo()
Julia Version 1.10.2
Commit bd47eca2c8a (2024-03-01 10:14 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
  CPU: 16 × AMD Ryzen 7 7840U w/ Radeon  780M Graphics
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-15.0.7 (ORCJIT, znver3)
Threads: 1 default, 0 interactive, 1 GC (on 16 virtual cores)
@KristofferC
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Can you try https://github.com/KristofferC/PkgFsck.jl

julia> import PkgFsck

julia> failures = PkgFsck.fsck_packages();

julia> failures_filtered = filter!(x->!x.has_build_file, failures)

and then if it finds something, run:

foreach(PkgFsck.redownload, failures_filtered)

@ufechner7
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Well, it finds something:

julia> failures
7-element Vector{PkgFsck.PkgFsckFailure}:
 PkgFsck.PkgFsckFailure("/home/ufechner/.julia/packages/PythonCall/wXfah", UUID("6099a3de-0909-46bc-b1f4-468b9a2dfc0d"), SHA1("4999b3e4e9bdeba0b61ede19cc45a2128db21cdc"), false)
 PkgFsck.PkgFsckFailure("/home/ufechner/.julia/packages/MATLAB/xBhSu", UUID("10e44e05-a98a-55b3-a45b-ba969058deb6"), SHA1("f640678d27790992e2a697f60e6afb1be3ebb7fc"), true)
 PkgFsck.PkgFsckFailure("/home/ufechner/.julia/packages/Conda/sDjAP", UUID("8f4d0f93-b110-5947-807f-2305c1781a2d"), SHA1("51cab8e982c5b598eea9c8ceaced4b58d9dd37c9"), true)
 PkgFsck.PkgFsckFailure("/home/ufechner/.julia/packages/MathLink/S39uA", UUID("18c93696-a329-5786-9845-8443133fa0b4"), SHA1("2883415fdc6db2d33640737bef634915c4a23c5d"), true)
 PkgFsck.PkgFsckFailure("/home/ufechner/.julia/packages/PyCall/1gn3u", UUID("438e738f-606a-5dbb-bf0a-cddfbfd45ab0"), SHA1("9816a3826b0ebf49ab4926e2b18842ad8b5c8f04"), true)
 PkgFsck.PkgFsckFailure("/home/ufechner/.julia/packages/PyCall/KLzIO", UUID("438e738f-606a-5dbb-bf0a-cddfbfd45ab0"), SHA1("1cb97fa63a3629c6d892af4f76fcc4ad8191837c"), true)
 PkgFsck.PkgFsckFailure("/home/ufechner/.julia/packages/HDF5/YX0jU", UUID("f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f"), SHA1("0b812e7872e2199a5a04944f486b4048944f1ed8"), true)

julia>

But this are not the packages for which I get the message "missing source file"...

@ufechner7
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Tried the same on a different computer, and getting a new error:

ufechner@ufryzen:~/repos/KiteUtils.jl$ jl
               _
   _       _ _(_)_     |  Documentation: https://docs.julialang.org
  (_)     | (_) (_)    |
   _ _   _| |_  __ _   |  Type "?" for help, "]?" for Pkg help.
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 1.10.2 (2024-03-01)
 _/ |\__'_|_|_|\__'_|  |  Official https://julialang.org/ release
|__/                   |

julia> using KiteUtils
    Updating registry at `~/.julia/registries/SpineRegistry`
    Updating git-repo `https://github.com/spine-tools/SpineJuliaRegistry`
    Updating registry at `~/.julia/registries/General.toml`
   Installed Preferences ──────── v1.4.3
   Installed PrecompileTools ──── v1.2.1
   Installed TranscodingStreams ─ v0.10.4
   Installed CSV ──────────────── v0.10.13
    Updating `~/repos/KiteUtils.jl/Project.toml`
  [69666777] + Arrow v2.7.1
  [336ed68f] + CSV v0.10.13
  [ffbed154] + DocStringExtensions v0.9.3
  [d96e819e] + Parameters v0.12.3
⌃ [731186ca] + RecursiveArrayTools v2.38.10
  [6038ab10] + Rotations v1.7.0
⌅ [90137ffa] + StaticArrays v1.5.12
  [09ab397b] + StructArrays v0.6.18
  [856f2bd8] + StructTypes v1.10.0
  [1e6cf692] + TestEnv v1.101.1
  [ddb6d928] + YAML v0.4.9
    Updating `~/repos/KiteUtils.jl/Manifest.toml`
⌅ [79e6a3ab] + Adapt v3.7.2
⌃ [4fba245c] + ArrayInterface v7.7.1
  [69666777] + Arrow v2.7.1
  [31f734f8] + ArrowTypes v2.3.0
  [c3b6d118] + BitIntegers v0.3.1
  [336ed68f] + CSV v0.10.13
  [5ba52731] + CodecLz4 v0.4.3
  [944b1d66] + CodecZlib v0.7.4
  [6b39b394] + CodecZstd v0.8.2
  [34da2185] + Compat v4.14.0
  [f0e56b4a] + ConcurrentUtilities v2.3.1
  [187b0558] + ConstructionBase v1.5.4
  [9a962f9c] + DataAPI v1.16.0
  [e2d170a0] + DataValueInterfaces v1.0.0
  [ffbed154] + DocStringExtensions v0.9.3
  [4e289a0a] + EnumX v1.0.4
  [e2ba6199] + ExprTools v0.1.10
  [48062228] + FilePathsBase v0.9.21
⌃ [46192b85] + GPUArraysCore v0.1.5
  [842dd82b] + InlineStrings v1.4.0
  [82899510] + IteratorInterfaceExtensions v1.0.0
  [692b3bcd] + JLLWrappers v1.5.0
  [e6f89c97] + LoggingExtras v1.0.3
  [78c3b35d] + Mocking v0.7.7
  [bac558e1] + OrderedCollections v1.6.3
  [d96e819e] + Parameters v0.12.3
  [69de0a69] + Parsers v2.8.1
  [2dfb63ee] + PooledArrays v1.4.3
  [aea7be01] + PrecompileTools v1.2.1
  [21216c6a] + Preferences v1.4.3
  [94ee1d12] + Quaternions v0.7.6
  [c1ae055f] + RealDot v0.1.0
  [3cdcf5f2] + RecipesBase v1.3.4
⌃ [731186ca] + RecursiveArrayTools v2.38.10
  [ae029012] + Requires v1.3.0
  [6038ab10] + Rotations v1.7.0
  [6c6a2e73] + Scratch v1.2.1
  [91c51154] + SentinelArrays v1.4.1
⌅ [90137ffa] + StaticArrays v1.5.12
  [1e83bf80] + StaticArraysCore v1.4.2
  [69024149] + StringEncodings v0.3.7
  [09ab397b] + StructArrays v0.6.18
  [856f2bd8] + StructTypes v1.10.0
⌅ [2efcf032] + SymbolicIndexingInterface v0.2.2
  [dc5dba14] + TZJData v1.1.0+2023d
  [3783bdb8] + TableTraits v1.0.1
  [bd369af6] + Tables v1.11.1
  [1e6cf692] + TestEnv v1.101.1
  [f269a46b] + TimeZones v1.13.0
  [3bb67fe8] + TranscodingStreams v0.10.4
  [3a884ed6] + UnPack v1.0.2
  [ea10d353] + WeakRefStrings v1.4.2
  [76eceee3] + WorkerUtilities v1.6.1
  [ddb6d928] + YAML v0.4.9
  [94ce4f54] + Libiconv_jll v1.17.0+0
  [5ced341a] + Lz4_jll v1.9.4+0
  [3161d3a3] + Zstd_jll v1.5.5+0
  [0dad84c5] + ArgTools v1.1.1
  [56f22d72] + Artifacts
  [2a0f44e3] + Base64
  [ade2ca70] + Dates
  [f43a241f] + Downloads v1.6.0
  [7b1f6079] + FileWatching
  [9fa8497b] + Future
  [b77e0a4c] + InteractiveUtils
  [4af54fe1] + LazyArtifacts
  [b27032c2] + LibCURL v0.6.4
  [76f85450] + LibGit2
  [8f399da3] + Libdl
  [37e2e46d] + LinearAlgebra
  [56ddb016] + Logging
  [d6f4376e] + Markdown
  [a63ad114] + Mmap
  [ca575930] + NetworkOptions v1.2.0
  [44cfe95a] + Pkg v1.10.0
  [de0858da] + Printf
  [3fa0cd96] + REPL
  [9a3f8284] + Random
  [ea8e919c] + SHA v0.7.0
  [9e88b42a] + Serialization
  [6462fe0b] + Sockets
  [2f01184e] + SparseArrays v1.10.0
  [10745b16] + Statistics v1.10.0
  [4607b0f0] + SuiteSparse
  [fa267f1f] + TOML v1.0.3
  [a4e569a6] + Tar v1.10.0
  [8dfed614] + Test
  [cf7118a7] + UUIDs
  [4ec0a83e] + Unicode
  [e66e0078] + CompilerSupportLibraries_jll v1.1.0+0
  [deac9b47] + LibCURL_jll v8.4.0+0
  [e37daf67] + LibGit2_jll v1.6.4+0
  [29816b5a] + LibSSH2_jll v1.11.0+1
  [c8ffd9c3] + MbedTLS_jll v2.28.2+1
  [14a3606d] + MozillaCACerts_jll v2023.1.10
  [4536629a] + OpenBLAS_jll v0.3.23+4
  [bea87d4a] + SuiteSparse_jll v7.2.1+1
  [83775a58] + Zlib_jll v1.2.13+1
  [8e850b90] + libblastrampoline_jll v5.8.0+1
  [8e850ede] + nghttp2_jll v1.52.0+1
  [3f19e933] + p7zip_jll v17.4.0+2
        Info Packages marked with ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. To see why use `status --outdated -m`
Precompiling KiteUtils
  ✗ StaticArrays
  19 dependencies successfully precompiled in 26 seconds. 18 already precompiled.

ERROR: The following 8 direct dependencies failed to precompile:

StaticArrays [90137ffa-7385-5640-81b9-e52037218182]

Failed to precompile StaticArrays [90137ffa-7385-5640-81b9-e52037218182] to "/home/ufechner/.julia/compiled/v1.10/StaticArrays/jl_CizKLM".
ERROR: LoadError: ArgumentError: Package StaticArrays does not have PrecompileTools in its dependencies:
- You may have a partially installed environment. Try `Pkg.instantiate()`
  to ensure all packages in the environment are installed.
- Or, if you have StaticArrays checked out for development and have
  added PrecompileTools as a dependency but haven't updated your primary
  environment's manifest file, try `Pkg.resolve()`.
- Otherwise you may need to report an issue with StaticArrays
Stacktrace:
 [1] macro expansion
   @ ./loading.jl:1776 [inlined]
 [2] macro expansion
   @ ./lock.jl:267 [inlined]
 [3] __require(into::Module, mod::Symbol)
   @ Base ./loading.jl:1753
 [4] #invoke_in_world#3
   @ ./essentials.jl:926 [inlined]
 [5] invoke_in_world
   @ ./essentials.jl:923 [inlined]
 [6] require(into::Module, mod::Symbol)
   @ Base ./loading.jl:1746
 [7] include
   @ ./Base.jl:495 [inlined]
 [8] 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:2222
 [9] top-level scope
   @ stdin:3
in expression starting at /home/ufechner/.julia/packages/StaticArrays/PLKkM/src/StaticArrays.jl:1
in expression starting at stdin:3
RecursiveArrayTools [731186ca-8d62-57ce-b412-fbd966d074cd]

Error: Missing source file for RecursiveArrayTools [731186ca-8d62-57ce-b412-fbd966d074cd]

Rotations [6038ab10-8711-5258-84ad-4b1120ba62dc]

Error: Missing source file for Rotations [6038ab10-8711-5258-84ad-4b1120ba62dc]

StructArrays [09ab397b-f2b6-538f-b94a-2f83cf4a842a]

Error: Missing source file for StructArrays [09ab397b-f2b6-538f-b94a-2f83cf4a842a]

YAML [ddb6d928-2868-570f-bddf-ab3f9cf99eb6]

Error: Missing source file for YAML [ddb6d928-2868-570f-bddf-ab3f9cf99eb6]

Parameters [d96e819e-fc66-5662-9728-84c9c7592b0a]

Error: Missing source file for Parameters [d96e819e-fc66-5662-9728-84c9c7592b0a]

StructTypes [856f2bd8-1eba-4b0a-8007-ebc267875bd4]

Error: Missing source file for StructTypes [856f2bd8-1eba-4b0a-8007-ebc267875bd4]

Arrow [69666777-d1a9-59fb-9406-91d4454c9d45]

Error: Missing source file for Arrow [69666777-d1a9-59fb-9406-91d4454c9d45]
Stacktrace:
  [1] pkgerror(msg::String)
    @ Pkg.Types ~/.julia/juliaup/julia-1.10.2+0.x64.linux.gnu/share/julia/stdlib/v1.10/Pkg/src/Types.jl:70
  [2] precompile(ctx::Pkg.Types.Context, pkgs::Vector{…}; internal_call::Bool, strict::Bool, warn_loaded::Bool, already_instantiated::Bool, timing::Bool, _from_loading::Bool, kwargs::@Kwargs{…})
    @ Pkg.API ~/.julia/juliaup/julia-1.10.2+0.x64.linux.gnu/share/julia/stdlib/v1.10/Pkg/src/API.jl:1659
  [3] precompile(pkgs::Vector{Pkg.Types.PackageSpec}; io::Base.TTY, kwargs::@Kwargs{_from_loading::Bool})
    @ Pkg.API ~/.julia/juliaup/julia-1.10.2+0.x64.linux.gnu/share/julia/stdlib/v1.10/Pkg/src/API.jl:159
  [4] precompile
    @ ~/.julia/juliaup/julia-1.10.2+0.x64.linux.gnu/share/julia/stdlib/v1.10/Pkg/src/API.jl:147 [inlined]
  [5] #precompile#114
    @ ~/.julia/juliaup/julia-1.10.2+0.x64.linux.gnu/share/julia/stdlib/v1.10/Pkg/src/API.jl:146 [inlined]
  [6] #invokelatest#2
    @ ./essentials.jl:894 [inlined]
  [7] invokelatest
    @ ./essentials.jl:889 [inlined]
  [8] _require(pkg::Base.PkgId, env::String)
    @ Base ./loading.jl:1963
  [9] __require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:1812
 [10] #invoke_in_world#3
    @ ./essentials.jl:926 [inlined]
 [11] invoke_in_world
    @ ./essentials.jl:923 [inlined]
 [12] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:1803
 [13] macro expansion
    @ ./loading.jl:1790 [inlined]
 [14] macro expansion
    @ ./lock.jl:267 [inlined]
 [15] __require(into::Module, mod::Symbol)
    @ Base ./loading.jl:1753
 [16] #invoke_in_world#3
    @ ./essentials.jl:926 [inlined]
 [17] invoke_in_world
    @ ./essentials.jl:923 [inlined]
 [18] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:1746
Some type information was truncated. Use `show(err)` to see complete types.

@lgoettgens
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On my arch linux system with julia 1.10.2, this error does not occur.
Your StaticArrays version (1.5.12) seems to be quite old, on my machine 1.9.3 was used.

@ufechner7
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ufechner7 commented Mar 12, 2024 •
edited
Loading

On my arch linux system with julia 1.10.2, this error does not occur. Your StaticArrays version (1.5.12) seems to be quite old, on my machine 1.9.3 was used.

Can you try again following my instructions:

git clone https://github.com/ufechner7/KiteUtils.jl

cd KiteUtils.jl
git checkout v0.4.8
julia --project

And then

using KiteUtils

The point is, I still have upstream project that depend on this older version of KiteUtils...

@lgoettgens
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julia> using KiteUtils
    Updating registry at `~/.julia/registries/General.toml`
   Installed GPUArraysCore ───────────── v0.1.5
   Installed Adapt ───────────────────── v3.7.2
   Installed SymbolicIndexingInterface ─ v0.2.2
   Installed RecursiveArrayTools ─────── v2.38.10
   Installed TestEnv ─────────────────── v1.101.1
    Updating `/tmp/KiteUtils.jl/Project.toml`
  [69666777] + Arrow v2.7.1
  [336ed68f] + CSV v0.10.13
  [ffbed154] + DocStringExtensions v0.9.3
  [d96e819e] + Parameters v0.12.3
⌃ [731186ca] + RecursiveArrayTools v2.38.10
  [6038ab10] + Rotations v1.7.0
  [90137ffa] + StaticArrays v1.9.3
  [09ab397b] + StructArrays v0.6.18
  [856f2bd8] + StructTypes v1.10.0
  [1e6cf692] + TestEnv v1.101.1
  [ddb6d928] + YAML v0.4.9
    Updating `/tmp/KiteUtils.jl/Manifest.toml`
⌅ [79e6a3ab] + Adapt v3.7.2
⌃ [4fba245c] + ArrayInterface v7.7.1
  [69666777] + Arrow v2.7.1
  [31f734f8] + ArrowTypes v2.3.0
  [c3b6d118] + BitIntegers v0.3.1
  [336ed68f] + CSV v0.10.13
  [5ba52731] + CodecLz4 v0.4.3
  [944b1d66] + CodecZlib v0.7.4
  [6b39b394] + CodecZstd v0.8.2
  [34da2185] + Compat v4.14.0
  [f0e56b4a] + ConcurrentUtilities v2.4.0
  [187b0558] + ConstructionBase v1.5.4
  [9a962f9c] + DataAPI v1.16.0
  [e2d170a0] + DataValueInterfaces v1.0.0
  [ffbed154] + DocStringExtensions v0.9.3
  [4e289a0a] + EnumX v1.0.4
  [e2ba6199] + ExprTools v0.1.10
  [48062228] + FilePathsBase v0.9.21
⌃ [46192b85] + GPUArraysCore v0.1.5
  [842dd82b] + InlineStrings v1.4.0
  [82899510] + IteratorInterfaceExtensions v1.0.0
  [692b3bcd] + JLLWrappers v1.5.0
  [e6f89c97] + LoggingExtras v1.0.3
  [78c3b35d] + Mocking v0.7.7
  [bac558e1] + OrderedCollections v1.6.3
  [d96e819e] + Parameters v0.12.3
  [69de0a69] + Parsers v2.8.1
  [2dfb63ee] + PooledArrays v1.4.3
  [aea7be01] + PrecompileTools v1.2.1
  [21216c6a] + Preferences v1.4.3
  [94ee1d12] + Quaternions v0.7.6
  [c1ae055f] + RealDot v0.1.0
  [3cdcf5f2] + RecipesBase v1.3.4
⌃ [731186ca] + RecursiveArrayTools v2.38.10
  [ae029012] + Requires v1.3.0
  [6038ab10] + Rotations v1.7.0
  [6c6a2e73] + Scratch v1.2.1
  [91c51154] + SentinelArrays v1.4.1
  [90137ffa] + StaticArrays v1.9.3
  [1e83bf80] + StaticArraysCore v1.4.2
  [69024149] + StringEncodings v0.3.7
  [09ab397b] + StructArrays v0.6.18
  [856f2bd8] + StructTypes v1.10.0
⌅ [2efcf032] + SymbolicIndexingInterface v0.2.2
  [dc5dba14] + TZJData v1.1.0+2023d
  [3783bdb8] + TableTraits v1.0.1
  [bd369af6] + Tables v1.11.1
  [1e6cf692] + TestEnv v1.101.1
  [f269a46b] + TimeZones v1.13.0
  [3bb67fe8] + TranscodingStreams v0.10.4
  [3a884ed6] + UnPack v1.0.2
  [ea10d353] + WeakRefStrings v1.4.2
  [76eceee3] + WorkerUtilities v1.6.1
  [ddb6d928] + YAML v0.4.9
  [94ce4f54] + Libiconv_jll v1.17.0+0
  [5ced341a] + Lz4_jll v1.9.4+0
  [3161d3a3] + Zstd_jll v1.5.5+0
  [0dad84c5] + ArgTools v1.1.1
  [56f22d72] + Artifacts
  [2a0f44e3] + Base64
  [ade2ca70] + Dates
  [f43a241f] + Downloads v1.6.0
  [7b1f6079] + FileWatching
  [9fa8497b] + Future
  [b77e0a4c] + InteractiveUtils
  [4af54fe1] + LazyArtifacts
  [b27032c2] + LibCURL v0.6.4
  [76f85450] + LibGit2
  [8f399da3] + Libdl
  [37e2e46d] + LinearAlgebra
  [56ddb016] + Logging
  [d6f4376e] + Markdown
  [a63ad114] + Mmap
  [ca575930] + NetworkOptions v1.2.0
  [44cfe95a] + Pkg v1.10.0
  [de0858da] + Printf
  [3fa0cd96] + REPL
  [9a3f8284] + Random
  [ea8e919c] + SHA v0.7.0
  [9e88b42a] + Serialization
  [6462fe0b] + Sockets
  [2f01184e] + SparseArrays v1.10.0
  [10745b16] + Statistics v1.10.0
  [4607b0f0] + SuiteSparse
  [fa267f1f] + TOML v1.0.3
  [a4e569a6] + Tar v1.10.0
  [8dfed614] + Test
  [cf7118a7] + UUIDs
  [4ec0a83e] + Unicode
  [e66e0078] + CompilerSupportLibraries_jll v1.1.0+0
  [deac9b47] + LibCURL_jll v8.4.0+0
  [e37daf67] + LibGit2_jll v1.6.4+0
  [29816b5a] + LibSSH2_jll v1.11.0+1
  [c8ffd9c3] + MbedTLS_jll v2.28.2+1
  [14a3606d] + MozillaCACerts_jll v2023.1.10
  [4536629a] + OpenBLAS_jll v0.3.23+4
  [bea87d4a] + SuiteSparse_jll v7.2.1+1
  [83775a58] + Zlib_jll v1.2.13+1
  [8e850b90] + libblastrampoline_jll v5.8.0+1
  [8e850ede] + nghttp2_jll v1.52.0+1
  [3f19e933] + p7zip_jll v17.4.0+2
        Info Packages marked with ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. To see why use `status --outdated -m`
Precompiling KiteUtils
  2 dependencies successfully precompiled in 10 seconds. 36 already precompiled.

ERROR: The following 8 direct dependencies failed to precompile:

CSV [336ed68f-0bac-5ca0-87d4-7b16caf5d00b]

Error: Missing source file for CSV [336ed68f-0bac-5ca0-87d4-7b16caf5d00b]
RecursiveArrayTools [731186ca-8d62-57ce-b412-fbd966d074cd]

Error: Missing source file for RecursiveArrayTools [731186ca-8d62-57ce-b412-fbd966d074cd]

Rotations [6038ab10-8711-5258-84ad-4b1120ba62dc]

Error: Missing source file for Rotations [6038ab10-8711-5258-84ad-4b1120ba62dc]

StructArrays [09ab397b-f2b6-538f-b94a-2f83cf4a842a]

Error: Missing source file for StructArrays [09ab397b-f2b6-538f-b94a-2f83cf4a842a]

Parameters [d96e819e-fc66-5662-9728-84c9c7592b0a]

Error: Missing source file for Parameters [d96e819e-fc66-5662-9728-84c9c7592b0a]

TestEnv [1e6cf692-eddd-4d53-88a5-2d735e33781b]

Error: Missing source file for TestEnv [1e6cf692-eddd-4d53-88a5-2d735e33781b]

StructTypes [856f2bd8-1eba-4b0a-8007-ebc267875bd4]

Error: Missing source file for StructTypes [856f2bd8-1eba-4b0a-8007-ebc267875bd4]

Arrow [69666777-d1a9-59fb-9406-91d4454c9d45]

Error: Missing source file for Arrow [69666777-d1a9-59fb-9406-91d4454c9d45]
Stacktrace:
  [1] pkgerror(msg::String)
    @ Pkg.Types ~/.julia/juliaup/julia-1.10.2+0.x64.linux.gnu/share/julia/stdlib/v1.10/Pkg/src/Types.jl:70
  [2] precompile(ctx::Pkg.Types.Context, pkgs::Vector{…}; internal_call::Bool, strict::Bool, warn_loaded::Bool, already_instantiated::Bool, timing::Bool, _from_loading::Bool, kwargs::@Kwargs{…})
    @ Pkg.API ~/.julia/juliaup/julia-1.10.2+0.x64.linux.gnu/share/julia/stdlib/v1.10/Pkg/src/API.jl:1659
  [3] precompile(pkgs::Vector{Pkg.Types.PackageSpec}; io::Base.TTY, kwargs::@Kwargs{_from_loading::Bool})
    @ Pkg.API ~/.julia/juliaup/julia-1.10.2+0.x64.linux.gnu/share/julia/stdlib/v1.10/Pkg/src/API.jl:159
  [4] precompile
    @ ~/.julia/juliaup/julia-1.10.2+0.x64.linux.gnu/share/julia/stdlib/v1.10/Pkg/src/API.jl:147 [inlined]
  [5] #precompile#114
    @ ~/.julia/juliaup/julia-1.10.2+0.x64.linux.gnu/share/julia/stdlib/v1.10/Pkg/src/API.jl:146 [inlined]
  [6] #invokelatest#2
    @ ./essentials.jl:894 [inlined]
  [7] invokelatest
    @ ./essentials.jl:889 [inlined]
  [8] _require(pkg::Base.PkgId, env::String)
    @ Base ./loading.jl:1963
  [9] __require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:1812
 [10] #invoke_in_world#3
    @ ./essentials.jl:926 [inlined]
 [11] invoke_in_world
    @ ./essentials.jl:923 [inlined]
 [12] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:1803
 [13] macro expansion
    @ ./loading.jl:1790 [inlined]
 [14] macro expansion
    @ ./lock.jl:267 [inlined]
 [15] __require(into::Module, mod::Symbol)
    @ Base ./loading.jl:1753
 [16] #invoke_in_world#3
    @ ./essentials.jl:926 [inlined]
 [17] invoke_in_world
    @ ./essentials.jl:923 [inlined]
 [18] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:1746
Some type information was truncated. Use `show(err)` to see complete types.

this looks very similar to your initial error

@KristofferC
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Member

I tried this too but couldn't get it to reproduce.

~/JuliaPkgs
❯ git clone https://github.com/ufechner7/KiteUtils.jl

cd KiteUtils.jl
git checkout v0.4.8
julia --project
Cloning into 'KiteUtils.jl'...
Note: switching to 'v0.4.8'.

HEAD is now at d172dcd Bump version to 0.4.8
               _
   _       _ _(_)_     |  Documentation: https://docs.julialang.org
  (_)     | (_) (_)    |
   _ _   _| |_  __ _   |  Type "?" for help, "]?" for Pkg help.
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 1.10.2 (2024-03-01)
 _/ |\__'_|_|_|\__'_|  |  Official https://julialang.org/ release
|__/                   |

julia> using KiteUtils
    Updating registry at `~/.julia/registries/General.toml`
   Installed Preferences ───────── v1.4.3
...
   Installed CodecZlib ─────────── v0.7.4
   Installed CodecLz4 ──────────── v0.4.3
   Installed CSV ───────────────── v0.10.13
  Downloaded artifact: tzjdata
  Downloaded artifact: Lz4
    Updating `~/JuliaPkgs/KiteUtils.jl/Project.toml`
  [69666777] + Arrow v2.7.1
  [336ed68f] + CSV v0.10.13
  [ffbed154] + DocStringExtensions v0.9.3
  [d96e819e] + Parameters v0.12.3
⌃ [731186ca] + RecursiveArrayTools v2.38.10
  [6038ab10] + Rotations v1.7.0
  [90137ffa] + StaticArrays v1.9.3
  [09ab397b] + StructArrays v0.6.18
  [856f2bd8] + StructTypes v1.10.0
  [1e6cf692] + TestEnv v1.101.1
  [ddb6d928] + YAML v0.4.9
    Updating `~/JuliaPkgs/KiteUtils.jl/Manifest.toml`
⌅ [79e6a3ab] + Adapt v3.7.2
⌃ [4fba245c] + ArrayInterface v7.7.1
...
  [09ab397b] + StructArrays v0.6.18
  [856f2bd8] + StructTypes v1.10.0
⌅ [2efcf032] + SymbolicIndexingInterface v0.2.2
  [dc5dba14] + TZJData v1.1.0+2023d
  [3783bdb8] + TableTraits v1.0.1
  [bd369af6] + Tables v1.11.1
...
        Info Packages marked with ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. To see why use `status --outdated -m`
Precompiling KiteUtils
  71 dependencies successfully precompiled in 21 seconds. 5 already precompiled.

julia> VERSION
v"1.10.2"

@ufechner7
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Author

I tried this too but couldn't get it to reproduce.

I did not see this error always, but often. Can you try to delete the folder KiteUtils.jl, checkout the code and try again?

@GunnarFarneback
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Contributor

Minor data point. I ran into the same kind of Missing source file errors on Julia 1.10.4 but for different packages. In this case PkgFsck, following #53623 (comment), found failures and redownloading solved the problem.

@benlorenz
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Contributor

benlorenz commented Aug 16, 2024 •
edited
Loading

I can reproduce the error, even with PkgFsck itself.
It seems to happen if one tries to call using SomePkg without a manifest file (but with pre-existing precompilation files):

lorenz@eddie /tmp $ git clone https://github.com/KristofferC/PkgFsck.jl
...
lorenz@eddie /tmp $ cd PkgFsck.jl/
lorenz@eddie /tmp/PkgFsck.jl $ rm Manifest.toml 
lorenz@eddie /tmp/PkgFsck.jl $ julia-latest --project=.
               _
   _       _ _(_)_     |  Documentation: https://docs.julialang.org
  (_)     | (_) (_)    |
   _ _   _| |_  __ _   |  Type "?" for help, "]?" for Pkg help.
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 1.10.4 (2024-06-04)
 _/ |\__'_|_|_|\__'_|  |  Official https://julialang.org/ release
|__/                   |

julia> using PkgFsck
    Updating registry at `~/.julia/registries/General`
    Updating git-repo `https://github.com/JuliaRegistries/General.git`
    Updating `/tmp/PkgFsck.jl/Project.toml`
  [c36e975a] + CoverageTools v1.3.2
  [f43a241f] ~ Downloads ⇒ v1.6.0
  [44cfe95a] ~ Pkg ⇒ v1.10.0
  [a4e569a6] ~ Tar ⇒ v1.10.0
    Updating `/tmp/PkgFsck.jl/Manifest.toml`
  [c36e975a] + CoverageTools v1.3.2
  [0dad84c5] + ArgTools v1.1.1
...
  [3f19e933] + p7zip_jll v17.4.0+2
Precompiling PkgFsck
  1 dependency successfully precompiled in 1 seconds

ERROR: The following 1 direct dependency failed to precompile:

CoverageTools [c36e975a-824b-4404-a568-ef97ca766997]

Error: Missing source file for CoverageTools [c36e975a-824b-4404-a568-ef97ca766997
Stacktrace:
  [1] pkgerror(msg::String)
    @ Pkg.Types ~/software/polymake/julia/julia/julia-1.10.4/share/julia/stdlib/v1.10/Pkg/src/Types.jl:70
  [2] precompile(ctx::Pkg.Types.Context, pkgs::Vector{…}; internal_call::Bool, strict::Bool, warn_loaded::Bool, already_instantiated::Bool, timing::Bool, _from_loading::Bool, kwargs::@Kwargs{…})
    @ Pkg.API ~/software/polymake/julia/julia/julia-1.10.4/share/julia/stdlib/v1.10/Pkg/src/API.jl:1659
  [3] precompile(pkgs::Vector{Pkg.Types.PackageSpec}; io::Base.TTY, kwargs::@Kwargs{_from_loading::Bool})
    @ Pkg.API ~/software/polymake/julia/julia/julia-1.10.4/share/julia/stdlib/v1.10/Pkg/src/API.jl:159
  [4] precompile
    @ ~/software/polymake/julia/julia/julia-1.10.4/share/julia/stdlib/v1.10/Pkg/src/API.jl:147 [inlined]
  [5] #precompile#114
    @ ~/software/polymake/julia/julia/julia-1.10.4/share/julia/stdlib/v1.10/Pkg/src/API.jl:146 [inlined]
  [6] #invokelatest#2
    @ ./essentials.jl:894 [inlined]
  [7] invokelatest
    @ ./essentials.jl:889 [inlined]
  [8] _require(pkg::Base.PkgId, env::String)
    @ Base ./loading.jl:1963
  [9] __require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:1812
 [10] #invoke_in_world#3
    @ ./essentials.jl:926 [inlined]
 [11] invoke_in_world
    @ ./essentials.jl:923 [inlined]
 [12] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:1803
 [13] macro expansion
    @ ./loading.jl:1790 [inlined]
 [14] macro expansion
    @ ./lock.jl:267 [inlined]
 [15] __require(into::Module, mod::Symbol)
    @ Base ./loading.jl:1753
 [16] #invoke_in_world#3
    @ ./essentials.jl:926 [inlined]
 [17] invoke_in_world
    @ ./essentials.jl:923 [inlined]
 [18] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:1746
Some type information was truncated. Use `show(err)` to see complete types.

Restarting julia and then loading the package works fine. Running ]resolve or ]up before using the package also avoids the error. But once the Manifest.toml is deleted again the next try to directly call using triggers the error again.

Edit: Another precondition for this to happen is that the precompile files for the package already exist, i.e. when .julia/compiled/v1.10/PkgFsck is removed the next load without a manifest works, but once the compiled file are there loading directly without a manifest errors.

@JamesWrigley JamesWrigley mentioned this issue Oct 9, 2024
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@nsajko nsajko added compiler:precompilation Precompilation of modules bug Indicates an unexpected problem or unintended behavior labels Oct 10, 2024
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bug Indicates an unexpected problem or unintended behavior compiler:precompilation Precompilation of modules
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@KristofferC @benlorenz @GunnarFarneback @ufechner7 @nsajko @lgoettgens