Package evaluation to load MoleculeView on Julia 1.14.0-DEV.87 (8bcaa34afa*) started at 2025-11-15T19:00:57.132 ################################################################################ # Set-up # Set-up completed after 0.1s ################################################################################ # Installation # Installing MoleculeView... Resolving package versions... Updating `~/.julia/environments/v1.14/Project.toml` [51e283bb] + MoleculeView v0.3.0 Updating `~/.julia/environments/v1.14/Manifest.toml` [621f4979] + AbstractFFTs v1.5.0 [1520ce14] + AbstractTrees v0.4.5 [79e6a3ab] + Adapt v4.4.0 [35492f91] + AdaptivePredicates v1.2.0 [66dad0bd] + AliasTables v1.1.3 [27a7e980] + Animations v0.4.2 [ec485272] + ArnoldiMethod v0.4.0 [4fba245c] + ArrayInterface v7.22.0 [67c07d97] + Automa v1.1.0 [13072b0f] + AxisAlgorithms v1.1.0 [39de3d68] + AxisArrays v0.4.8 [18cc8868] + BaseDirs v1.3.2 [d1d4a3ce] + BitFlags v0.1.9 [62783981] + BitTwiddlingConvenienceFunctions v0.1.6 [824d6782] + Bonito v4.1.11 [fa961155] + CEnum v0.5.0 [2a0fbf3d] + CPUSummary v0.2.7 [96374032] + CRlibm v1.0.2 [aafaddc9] + CatIndices v0.2.2 [d360d2e6] + ChainRulesCore v1.26.0 [0b6fb165] + ChunkCodecCore v1.0.0 [4c0bbee4] + ChunkCodecLibZlib v1.0.0 [55437552] + ChunkCodecLibZstd v1.0.0 [fb6a15b2] + CloseOpenIntervals v0.1.13 [aaaa29a8] + Clustering v0.15.8 [944b1d66] + CodecZlib v0.7.8 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v1.11.0 [ade2ca70] + Dates v1.11.0 [8ba89e20] + Distributed v1.11.0 [f43a241f] + Downloads v1.7.0 [7b1f6079] + FileWatching v1.11.0 [9fa8497b] + Future v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.12.0 [4af54fe1] + LazyArtifacts v1.11.0 [b27032c2] + LibCURL v1.0.0 [76f85450] + LibGit2 v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.13.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap v1.11.0 [ca575930] + NetworkOptions v1.3.0 [44cfe95a] + Pkg v1.13.0 [de0858da] + Printf v1.11.0 [3fa0cd96] + REPL v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v1.0.0 [9e88b42a] + Serialization v1.11.0 [1a1011a3] + SharedArrays v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.13.0 [f489334b] + StyledStrings v1.11.0 [4607b0f0] + SuiteSparse [fa267f1f] + TOML v1.0.3 [a4e569a6] + Tar v1.10.0 [8dfed614] + Test v1.11.0 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1 [deac9b47] + LibCURL_jll v8.16.0+0 [e37daf67] + LibGit2_jll v1.9.1+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.11.4 [4536629a] + OpenBLAS_jll v0.3.29+0 [05823500] + OpenLibm_jll v0.8.7+0 [458c3c95] + OpenSSL_jll v3.5.4+0 [efcefdf7] + PCRE2_jll v10.47.0+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.1+2 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850b90] + libblastrampoline_jll v5.15.0+0 [8e850ede] + nghttp2_jll v1.68.0+1 [3f19e933] + p7zip_jll v17.7.0+0 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` Installation completed after 6.51s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Project No packages added to or removed from `~/.julia/environments/pkgeval/Project.toml` Manifest No packages added to or removed from `~/.julia/environments/pkgeval/Manifest.toml` Precompiling package dependencies... Precompiling packages... 9321.3 ms ✓ Colors 1855.7 ms ✓ Hyperscript 91024.4 ms ✓ DataFrames 1364.0 ms ✓ Deno_jll 1549.6 ms ✓ RegionTrees 37336.2 ms ✓ Polynomials 9936.4 ms ✓ Graphs 51205.7 ms ✓ TiffImages 2654.7 ms ✓ Packing 11294.4 ms ✓ GridLayoutBase 7116.2 ms ✓ MakieCore 3510.1 ms ✓ ShaderAbstractions 25710.8 ms ✓ PythonCall 4414.7 ms ✓ KernelDensity 10683.9 ms ✓ DelaunayTriangulation 1357.8 ms ✓ Animations 5433.0 ms ✓ OpenEXR 1302.9 ms ✓ Graphics 4179.5 ms ✓ ColorBrewer 27348.6 ms ✓ ImageCore 5189.4 ms ✓ FreeTypeAbstraction 9267.4 ms ✓ ColorSchemes ERROR: LoadError: ArgumentError: Cannot load (`using/import`) module SHA into module Bonito in package Bonito because package Bonito does not have SHA in its dependencies: - Note that the following manifests in the load path were resolved with a potentially  different DEV version of the current version, which may be the cause of the error.  Try to re-resolve them in the current version, or consider deleting them if that fails:  /home/pkgeval/.julia/environments/v1.14/Manifest.toml - You may have a partially installed environment. Try `Pkg.instantiate()`  to ensure all packages in the environment are installed. - Or, if you have Bonito checked out for development and have  added SHA 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 Bonito Stacktrace:  [1] macro expansion  @ ./loading.jl:2488 [inlined]  [2] macro expansion  @ ./lock.jl:376 [inlined]  [3] __require(into::Module, mod::Symbol)  @ Base ./loading.jl:2468  [4] require  @ ./loading.jl:2444 [inlined]  [5] eval_import_path  @ ./module.jl:36 [inlined]  [6] eval_import_path_all(at::Module, path::Expr, keyword::String)  @ Base ./module.jl:60  [7] _eval_using  @ ./module.jl:137 [inlined]  [8] _eval_using(to::Module, path::Expr)  @ Base ./module.jl:137  [9] top-level scope  @ ~/.julia/packages/Bonito/18mTs/src/Bonito.jl:18  [10] include(mod::Module, _path::String)  @ Base ./Base.jl:309  [11] 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:3148  [12] top-level scope  @ stdin:5  [13] eval(m::Module, e::Any)  @ Core ./boot.jl:489  [14] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)  @ Base ./loading.jl:2994  [15] include_string  @ ./loading.jl:3004 [inlined]  [16] exec_options(opts::Base.JLOptions)  @ Base ./client.jl:342  [17] _start()  @ Base ./client.jl:577 in expression starting at /home/pkgeval/.julia/packages/Bonito/18mTs/src/Bonito.jl:1 in expression starting at stdin:5 Precompilation completed after 341.89s ################################################################################ # Loading # Loading MoleculeView... ERROR: LoadError: ArgumentError: Cannot load (`using/import`) module SHA into module Bonito in package Bonito because package Bonito does not have SHA in its dependencies: - Note that the following manifests in the load path were resolved with a potentially  different DEV version of the current version, which may be the cause of the error.  Try to re-resolve them in the current version, or consider deleting them if that fails:  /home/pkgeval/.julia/environments/v1.14/Manifest.toml - You may have a partially installed environment. Try `Pkg.instantiate()`  to ensure all packages in the environment are installed. - Or, if you have Bonito checked out for development and have  added SHA 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 Bonito Stacktrace:  [1] macro expansion  @ ./loading.jl:2488 [inlined]  [2] macro expansion  @ ./lock.jl:376 [inlined]  [3] __require(into::Module, mod::Symbol)  @ Base ./loading.jl:2468  [4] require  @ ./loading.jl:2444 [inlined]  [5] eval_import_path  @ ./module.jl:36 [inlined]  [6] eval_import_path_all(at::Module, path::Expr, keyword::String)  @ Base ./module.jl:60  [7] _eval_using  @ ./module.jl:137 [inlined]  [8] _eval_using(to::Module, path::Expr)  @ Base ./module.jl:137  [9] top-level scope  @ ~/.julia/packages/Bonito/18mTs/src/Bonito.jl:18  [10] include(mod::Module, _path::String)  @ Base ./Base.jl:309  [11] 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:3148  [12] top-level scope  @ stdin:5  [13] eval(m::Module, e::Any)  @ Core ./boot.jl:489  [14] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)  @ Base ./loading.jl:2994  [15] include_string  @ ./loading.jl:3004 [inlined]  [16] exec_options(opts::Base.JLOptions)  @ Base ./client.jl:342  [17] _start()  @ Base ./client.jl:577 in expression starting at /home/pkgeval/.julia/packages/Bonito/18mTs/src/Bonito.jl:1 in expression starting at stdin:5  CondaPkg Found dependencies: /home/pkgeval/.julia/packages/CondaPkg/0UqYV/CondaPkg.toml  CondaPkg Found dependencies: /home/pkgeval/.julia/packages/MoleculeFlow/5xJwa/CondaPkg.toml  CondaPkg Found dependencies: /home/pkgeval/.julia/packages/PythonCall/Ds20G/CondaPkg.toml  CondaPkg Resolving changes  + openssl  + python  + rdkit (pip)  + uv  CondaPkg Initialising pixi  │ /home/pkgeval/.julia/artifacts/cefba4912c2b400756d043a2563ef77a0088866b/bin/pixi  │ init  │ --format pixi  └ /home/pkgeval/.julia/environments/v1.14/.CondaPkg ✔ Created /home/pkgeval/.julia/environments/v1.14/.CondaPkg/pixi.toml  CondaPkg Wrote /home/pkgeval/.julia/environments/v1.14/.CondaPkg/pixi.toml  │ [dependencies]  │ openssl = ">=3, <3.6"  │ uv = ">=0.4"  │  │ [dependencies.python]  │ version = ">=3.10,<4"  │ build = "*cp*"  │ channel = "conda-forge"  │  │ [pypi-dependencies]  │ rdkit = "==2025.03.6"  │  │ [project]  │ name = ".CondaPkg"  │ description = "automatically generated by CondaPkg.jl"  │ platforms = ["linux-64"]  │ channel-priority = "strict"  └ channels = ["conda-forge"]  CondaPkg Installing packages  │ /home/pkgeval/.julia/artifacts/cefba4912c2b400756d043a2563ef77a0088866b/bin/pixi  │ install  └ --manifest-path /home/pkgeval/.julia/environments/v1.14/.CondaPkg/pixi.toml ✔ The default environment has been installed. 1 dependency had output during precompilation: ┌ MoleculeFlow │ [Output was shown above] └ ERROR: LoadError: ArgumentError: Cannot load (`using/import`) module SHA into module Bonito in package Bonito because package Bonito does not have SHA in its dependencies: - Note that the following manifests in the load path were resolved with a potentially  different DEV version of the current version, which may be the cause of the error.  Try to re-resolve them in the current version, or consider deleting them if that fails:  /home/pkgeval/.julia/environments/v1.14/Manifest.toml - You may have a partially installed environment. Try `Pkg.instantiate()`  to ensure all packages in the environment are installed. - Or, if you have Bonito checked out for development and have  added SHA 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 Bonito Stacktrace:  [1] macro expansion  @ ./loading.jl:2488 [inlined]  [2] macro expansion  @ ./lock.jl:376 [inlined]  [3] __require(into::Module, mod::Symbol)  @ Base ./loading.jl:2468  [4] require  @ ./loading.jl:2444 [inlined]  [5] eval_import_path  @ ./module.jl:36 [inlined]  [6] eval_import_path_all(at::Module, path::Expr, keyword::String)  @ Base ./module.jl:60  [7] _eval_using  @ ./module.jl:137 [inlined]  [8] _eval_using(to::Module, path::Expr)  @ Base ./module.jl:137  [9] top-level scope  @ ~/.julia/packages/Bonito/18mTs/src/Bonito.jl:18  [10] include(mod::Module, _path::String)  @ Base ./Base.jl:309  [11] 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:3148  [12] top-level scope  @ stdin:5  [13] eval(m::Module, e::Any)  @ Core ./boot.jl:489  [14] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)  @ Base ./loading.jl:2994  [15] include_string  @ ./loading.jl:3004 [inlined]  [16] exec_options(opts::Base.JLOptions)  @ Base ./client.jl:342  [17] _start()  @ Base ./client.jl:577 in expression starting at /home/pkgeval/.julia/packages/Bonito/18mTs/src/Bonito.jl:1 in expression starting at stdin:5 ERROR: LoadError: ArgumentError: Cannot load (`using/import`) module SHA into module Bonito in package Bonito because package Bonito does not have SHA in its dependencies: - Note that the following manifests in the load path were resolved with a potentially  different DEV version of the current version, which may be the cause of the error.  Try to re-resolve them in the current version, or consider deleting them if that fails:  /home/pkgeval/.julia/environments/v1.14/Manifest.toml - You may have a partially installed environment. Try `Pkg.instantiate()`  to ensure all packages in the environment are installed. - Or, if you have Bonito checked out for development and have  added SHA 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 Bonito Stacktrace:  [1] macro expansion  @ ./loading.jl:2488 [inlined]  [2] macro expansion  @ ./lock.jl:376 [inlined]  [3] __require(into::Module, mod::Symbol)  @ Base ./loading.jl:2468  [4] require  @ ./loading.jl:2444 [inlined]  [5] eval_import_path  @ ./module.jl:36 [inlined]  [6] eval_import_path_all(at::Module, path::Expr, keyword::String)  @ Base ./module.jl:60  [7] _eval_using  @ ./module.jl:137 [inlined]  [8] _eval_using(to::Module, path::Expr)  @ Base ./module.jl:137  [9] top-level scope  @ ~/.julia/packages/Bonito/18mTs/src/Bonito.jl:18  [10] include(mod::Module, _path::String)  @ Base ./Base.jl:309  [11] 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:3148  [12] top-level scope  @ stdin:5  [13] eval(m::Module, e::Any)  @ Core ./boot.jl:489  [14] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)  @ Base ./loading.jl:2994  [15] include_string  @ ./loading.jl:3004 [inlined]  [16] exec_options(opts::Base.JLOptions)  @ Base ./client.jl:342  [17] _start()  @ Base ./client.jl:577 in expression starting at /home/pkgeval/.julia/packages/Bonito/18mTs/src/Bonito.jl:1 in expression starting at stdin:5 1 dependency had output during precompilation: ┌ Bonito │ [Output was shown above] └ ERROR: LoadError: The following 1 package failed to precompile: Bonito Failed to precompile Bonito [824d6782-a2ef-11e9-3a09-e5662e0c26f8] to "/home/pkgeval/.julia/compiled/v1.14/Bonito/jl_XCEkYB" (ProcessExited(1)). in expression starting at /home/pkgeval/.julia/packages/WGLMakie/KlHpR/src/WGLMakie.jl:1 in expression starting at /home/pkgeval/.julia/packages/MoleculeView/lrfKI/src/scatter/interactive_scatter.jl:1 in expression starting at /home/pkgeval/.julia/packages/MoleculeView/lrfKI/src/MoleculeView.jl:1 Loading failed after 537.07s ERROR: LoadError: failed process: Process(`/opt/julia/bin/julia -C native -J/opt/julia/lib/julia/sys.so -g1 --check-bounds=yes --inline=yes --pkgimages=existing -e 'using MoleculeView'`, ProcessExited(1)) [1] Stacktrace: [1] pipeline_error @ ./process.jl:611 [inlined] [2] run(::Cmd; wait::Bool) @ Base ./process.jl:526 [3] run(::Cmd) @ Base ./process.jl:523 [4] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:193 [5] include(mod::Module, _path::String) @ Base ./Base.jl:309 [6] exec_options(opts::Base.JLOptions) @ Base ./client.jl:344 [7] _start() @ Base ./client.jl:577 in expression starting at /PkgEval.jl/scripts/evaluate.jl:184 PkgEval failed after 906.54s: package fails to precompile