Package evaluation to test SingleCellProjections on Julia 1.14.0-DEV.1299 (6d6224db99*) started at 2025-11-27T20:46:51.411 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 10.19s ################################################################################ # Installation # Installing SingleCellProjections... Resolving package versions... Installed Rmath_jll ─────────────────── v0.5.1+0 Installed CompositionsBase ──────────── v0.1.2 Installed CommonSolve ───────────────── v0.2.4 Installed DiffResults ───────────────── v1.1.0 Installed MacroTools ────────────────── v0.5.16 Installed DataStructures ────────────── v0.18.22 Installed ForwardDiff ───────────────── v1.3.0 Installed StableHashTraits ──────────── v2.0.2 Installed FillArrays ────────────────── v1.15.0 Installed InlineStrings ─────────────── v1.4.5 Installed libaec_jll ────────────────── v1.1.4+0 Installed Lz4_jll ───────────────────── v1.10.1+0 Installed AbstractTrees ─────────────── v0.4.5 Installed Adapt ─────────────────────── v4.4.0 Installed ConstructionBase ──────────── v1.6.0 Installed MPICH_jll ─────────────────── v4.3.2+0 Installed HypergeometricFunctions ───── v0.3.28 Installed AliasTables ───────────────── v1.1.3 Installed DelimitedFiles ────────────── v1.9.1 Installed SCTransform ───────────────── v0.3.1 Installed StatsBase ─────────────────── v0.34.8 Installed SingleCellProjections ─────── v0.4.4 Installed Optim ─────────────────────── v1.13.3 Installed CodecZlib ─────────────────── v0.7.8 Installed MicrosoftMPI_jll ──────────── v10.1.4+3 Installed NearestNeighbors ──────────── v0.4.24 Installed OrderedCollections ────────── v1.8.1 Installed ArrayInterface ────────────── v7.22.0 Installed TranscodingStreams ────────── v0.11.3 Installed Compat ────────────────────── v4.18.1 Installed IteratorInterfaceExtensions ─ v1.0.0 Installed DataAPI ───────────────────── v1.16.0 Installed InvertedIndices ───────────── v1.3.1 Installed Blosc ─────────────────────── v0.7.3 Installed PositiveFactorizations ────── v0.2.4 Installed Statistics ────────────────── v1.11.1 Installed PrecompileTools ───────────── v1.3.3 Installed Xorg_libpciaccess_jll ─────── v0.18.1+0 Installed DataValueInterfaces ───────── v1.0.0 Installed StatsAPI ──────────────────── v1.7.1 Installed ProgressMeter ─────────────── v1.11.0 Installed SentinelArrays ────────────── v1.4.8 Installed CommonSubexpressions ──────── v0.3.1 Installed SingleCell10x ─────────────── v0.2.2 Installed StaticArrays ──────────────── v1.9.15 Installed Blosc_jll ─────────────────── v1.21.7+0 Installed StaticArraysCore ──────────── v1.4.4 Installed IrrationalConstants ───────── v0.2.6 Installed TupleTools ────────────────── v1.6.0 Installed Distances ─────────────────── v0.10.12 Installed NaNMath ───────────────────── v1.1.3 Installed QuadGK ────────────────────── v2.11.2 Installed StringManipulation ────────── v0.4.2 Installed OpenSpecFun_jll ───────────── v0.5.6+0 Installed Requires ──────────────────── v1.3.1 Installed HDF5_jll ──────────────────── v1.14.6+0 Installed LogExpFunctions ───────────── v0.3.29 Installed DiffRules ─────────────────── v1.15.1 Installed OpenMPI_jll ───────────────── v5.0.9+0 Installed Roots ─────────────────────── v2.2.10 Installed Hwloc_jll ─────────────────── v2.12.2+0 Installed ThreadedSparseArrays ──────── v0.2.3 Installed FiniteDiff ────────────────── v2.29.0 Installed PrettyTables ──────────────── v3.1.2 Installed Rmath ─────────────────────── v0.9.0 Installed Distributions ─────────────── v0.25.122 Installed StatsFuns ─────────────────── v1.5.2 Installed PtrArrays ─────────────────── v1.3.0 Installed Tables ────────────────────── v1.12.1 Installed XML2_jll ──────────────────── v2.13.9+0 Installed EnumX ─────────────────────── v1.0.5 Installed NLSolversBase ─────────────── v7.10.0 Installed Scratch ───────────────────── v1.3.0 Installed Reexport ──────────────────── v1.2.2 Installed DataFrames ────────────────── v1.8.1 Installed InverseFunctions ──────────── v0.1.17 Installed SpecialFunctions ──────────── v2.6.1 Installed H5Zblosc ──────────────────── v0.1.2 Installed Setfield ──────────────────── v1.1.2 Installed Preferences ───────────────── v1.5.0 Installed Missings ──────────────────── v1.2.0 Installed PooledArrays ──────────────── v1.4.3 Installed JLLWrappers ───────────────── v1.7.1 Installed MPIPreferences ────────────── v0.1.11 Installed TableTraits ───────────────── v1.0.1 Installed Libiconv_jll ──────────────── v1.18.0+0 Installed LaTeXStrings ──────────────── v1.4.0 Installed PDMats ────────────────────── v0.11.36 Installed Crayons ───────────────────── v4.1.1 Installed SortingAlgorithms ─────────── v1.2.2 Installed StructTypes ───────────────── v1.11.0 Installed MPItrampoline_jll ─────────── v5.5.4+0 Installed LineSearches ──────────────── v7.5.1 Installed KernelDensitySJ ───────────── v0.2.1 Installed HDF5 ──────────────────────── v0.17.2 Installed ADTypes ───────────────────── v1.19.0 Installed DocStringExtensions ───────── v0.9.5 Installed Accessors ─────────────────── v0.1.42 Installed DifferentiationInterface ──── v0.7.12 Installing 11 artifacts Installed artifact Xorg_libpciaccess 24.8 KiB Installed artifact libaec 49.6 KiB Installed artifact OpenSpecFun 194.9 KiB Installed artifact Rmath 121.9 KiB Installed artifact Blosc 44.2 KiB Installed artifact Lz4 239.7 KiB Installed artifact Libiconv 1.9 MiB Installed artifact HDF5 5.7 MiB Installed artifact MPICH 3.3 MiB Installed artifact Hwloc 3.5 MiB Installed artifact XML2 2.5 MiB Updating `~/.julia/environments/v1.14/Project.toml` [03d38035] + SingleCellProjections v0.4.4 Updating `~/.julia/environments/v1.14/Manifest.toml` [47edcb42] + ADTypes v1.19.0 [1520ce14] + AbstractTrees v0.4.5 [7d9f7c33] + Accessors v0.1.42 [79e6a3ab] + Adapt v4.4.0 [66dad0bd] + AliasTables v1.1.3 [4fba245c] + ArrayInterface v7.22.0 [a74b3585] + Blosc v0.7.3 [944b1d66] + CodecZlib v0.7.8 [38540f10] + CommonSolve v0.2.4 [bbf7d656] + CommonSubexpressions v0.3.1 [34da2185] + Compat v4.18.1 [a33af91c] + CompositionsBase v0.1.2 [187b0558] + ConstructionBase v1.6.0 [a8cc5b0e] + Crayons v4.1.1 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.8.1 ⌅ [864edb3b] + DataStructures v0.18.22 [e2d170a0] + DataValueInterfaces v1.0.0 [8bb1440f] + DelimitedFiles v1.9.1 [163ba53b] + DiffResults v1.1.0 [b552c78f] + DiffRules v1.15.1 [a0c0ee7d] + DifferentiationInterface v0.7.12 [b4f34e82] + Distances v0.10.12 [31c24e10] + Distributions v0.25.122 [ffbed154] + DocStringExtensions v0.9.5 [4e289a0a] + EnumX v1.0.5 [1a297f60] + FillArrays v1.15.0 [6a86dc24] + FiniteDiff v2.29.0 [f6369f11] + ForwardDiff v1.3.0 [c8ec2601] + H5Zblosc v0.1.2 [f67ccb44] + HDF5 v0.17.2 [34004b35] + HypergeometricFunctions v0.3.28 [842dd82b] + InlineStrings v1.4.5 [3587e190] + InverseFunctions v0.1.17 [41ab1584] + InvertedIndices v1.3.1 [92d709cd] + IrrationalConstants v0.2.6 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] + JLLWrappers v1.7.1 [49dc5b4e] + KernelDensitySJ v0.2.1 [b964fa9f] + LaTeXStrings v1.4.0 [d3d80556] + LineSearches v7.5.1 [2ab3a3ac] + LogExpFunctions v0.3.29 [3da0fdf6] + MPIPreferences v0.1.11 [1914dd2f] + MacroTools v0.5.16 [e1d29d7a] + Missings v1.2.0 [d41bc354] + NLSolversBase v7.10.0 [77ba4419] + NaNMath v1.1.3 [b8a86587] + NearestNeighbors v0.4.24 [429524aa] + Optim v1.13.3 [bac558e1] + OrderedCollections v1.8.1 [90014a1f] + PDMats v0.11.36 [2dfb63ee] + PooledArrays v1.4.3 [85a6dd25] + PositiveFactorizations v0.2.4 [aea7be01] + PrecompileTools v1.3.3 [21216c6a] + Preferences v1.5.0 [08abe8d2] + PrettyTables v3.1.2 [92933f4c] + ProgressMeter v1.11.0 [43287f4e] + PtrArrays v1.3.0 [1fd47b50] + QuadGK v2.11.2 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [79098fc4] + Rmath v0.9.0 [f2b01f46] + Roots v2.2.10 [f56ea72b] + SCTransform v0.3.1 [6c6a2e73] + Scratch v1.3.0 [91c51154] + SentinelArrays v1.4.8 [efcf1570] + Setfield v1.1.2 [eddce310] + SingleCell10x v0.2.2 [03d38035] + SingleCellProjections v0.4.4 [a2af1166] + SortingAlgorithms v1.2.2 [276daf66] + SpecialFunctions v2.6.1 [c5dd0088] + StableHashTraits v2.0.2 [90137ffa] + StaticArrays v1.9.15 [1e83bf80] + StaticArraysCore v1.4.4 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.7.1 [2913bbd2] + StatsBase v0.34.8 [4c63d2b9] + StatsFuns v1.5.2 [892a3eda] + StringManipulation v0.4.2 [856f2bd8] + StructTypes v1.11.0 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [59d54670] + ThreadedSparseArrays v0.2.3 [3bb67fe8] + TranscodingStreams v0.11.3 [9d95972d] + TupleTools v1.6.0 [0b7ba130] + Blosc_jll v1.21.7+0 ⌅ [0234f1f7] + HDF5_jll v1.14.6+0 [e33a78d0] + Hwloc_jll v2.12.2+0 [94ce4f54] + Libiconv_jll v1.18.0+0 [5ced341a] + Lz4_jll v1.10.1+0 [7cb0a576] + MPICH_jll v4.3.2+0 [f1f71cc9] + MPItrampoline_jll v5.5.4+0 [9237b28f] + MicrosoftMPI_jll v10.1.4+3 [fe0851c0] + OpenMPI_jll v5.0.9+0 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [f50d1b31] + Rmath_jll v0.5.1+0 ⌅ [02c8fc9c] + XML2_jll v2.13.9+0 [a65dc6b1] + Xorg_libpciaccess_jll v0.18.1+0 [477f73a3] + libaec_jll v1.1.4+0 [0dad84c5] + ArgTools v1.1.2 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 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 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.13.0 [f489334b] + StyledStrings v1.13.0 [4607b0f0] + SuiteSparse [fa267f1f] + TOML v1.0.3 [a4e569a6] + Tar v1.10.0 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1 [deac9b47] + LibCURL_jll v8.17.0+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 ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Installation completed after 15.5s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... WARNING: Imported binding Operations.project_rel_path was undeclared at import time during import to TestEnv. 5064.7 ms ✓ TestEnv 1 dependency successfully precompiled in 5 seconds. 27 already precompiled. 1 dependency had output during precompilation: ┌ TestEnv │ WARNING: Imported binding Operations.project_rel_path was undeclared at import time during import to TestEnv. └ ┌ Error: Failed to use TestEnv.jl; test dependencies will not be precompiled │ exception = │ UndefVarError: `project_rel_path` not defined in `TestEnv` │ Suggestion: this global was defined as `Pkg.Operations.project_rel_path` but not assigned a value. │ Stacktrace: │ [1] get_test_dir(ctx::Pkg.Types.Context, pkgspec::PackageSpec) │ @ TestEnv ~/.julia/packages/TestEnv/i9lgt/src/julia-1.11/common.jl:75 │ [2] test_dir_has_project_file │ @ ~/.julia/packages/TestEnv/i9lgt/src/julia-1.11/common.jl:52 [inlined] │ [3] maybe_gen_project_override! │ @ ~/.julia/packages/TestEnv/i9lgt/src/julia-1.11/common.jl:83 [inlined] │ [4] activate(pkg::String; allow_reresolve::Bool) │ @ TestEnv ~/.julia/packages/TestEnv/i9lgt/src/julia-1.11/activate_set.jl:12 │ [5] activate(pkg::String) │ @ TestEnv ~/.julia/packages/TestEnv/i9lgt/src/julia-1.11/activate_set.jl:9 │ [6] top-level scope │ @ /PkgEval.jl/scripts/precompile.jl:24 │ [7] include(mod::Module, _path::String) │ @ Base ./Base.jl:309 │ [8] exec_options(opts::Base.JLOptions) │ @ Base ./client.jl:344 │ [9] _start() │ @ Base ./client.jl:577 └ @ Main /PkgEval.jl/scripts/precompile.jl:26 Precompiling package dependencies... Precompiling packages... 4512.8 ms ✓ MacroTools 1679.2 ms ✓ InlineStrings 783.9 ms ✓ Reexport 1106.4 ms ✓ ConstructionBase 2072.2 ms ✓ IrrationalConstants 744.6 ms ✓ DataValueInterfaces 836.3 ms ✓ StatsAPI 1000.4 ms ✓ TupleTools 784.6 ms ✓ CommonSolve 1292.9 ms ✓ TranscodingStreams 847.0 ms ✓ LaTeXStrings 1140.3 ms ✓ Statistics 1009.5 ms ✓ StaticArraysCore 821.7 ms ✓ PtrArrays 973.6 ms ✓ PositiveFactorizations 914.5 ms ✓ DataAPI 959.7 ms ✓ InvertedIndices 912.4 ms ✓ InverseFunctions 829.9 ms ✓ CompositionsBase 1141.6 ms ✓ AbstractTrees 877.2 ms ✓ EnumX 2185.4 ms ✓ FillArrays 1362.3 ms ✓ OrderedCollections 1394.6 ms ✓ ADTypes 1082.0 ms ✓ DocStringExtensions 756.6 ms ✓ IteratorInterfaceExtensions 1848.4 ms ✓ Crayons 965.3 ms ✓ DelimitedFiles 1011.7 ms ✓ NaNMath 1186.5 ms ✓ Requires 1237.7 ms ✓ SuiteSparse 1609.3 ms ✓ ThreadedSparseArrays 923.4 ms ✓ Scratch 2907.4 ms ✓ SentinelArrays 1656.0 ms ✓ StructTypes 1805.3 ms ✓ ProgressMeter 1172.4 ms ✓ Compat 1162.0 ms ✓ Preferences 1795.1 ms ✓ CommonSubexpressions 802.5 ms ✓ ConstructionBase → ConstructionBaseLinearAlgebraExt 974.7 ms ✓ CodecZlib 1322.1 ms ✓ Statistics → SparseArraysExt 1467.0 ms ✓ Distances 852.5 ms ✓ DiffResults 1002.8 ms ✓ AliasTables 965.1 ms ✓ Missings 1008.5 ms ✓ PooledArrays 864.8 ms ✓ InverseFunctions → InverseFunctionsDatesExt 780.1 ms ✓ CompositionsBase → CompositionsBaseInverseFunctionsExt 1501.2 ms ✓ FillArrays → FillArraysSparseArraysExt 935.9 ms ✓ FillArrays → FillArraysStatisticsExt 762.8 ms ✓ ADTypes → ADTypesConstructionBaseExt 1854.9 ms ✓ DifferentiationInterface 1455.8 ms ✓ LogExpFunctions 756.2 ms ✓ TableTraits 952.4 ms ✓ Adapt 1840.9 ms ✓ PDMats 836.1 ms ✓ Compat → CompatLinearAlgebraExt 919.2 ms ✓ PrecompileTools 1173.3 ms ✓ JLLWrappers 1416.1 ms ✓ MPIPreferences 2978.7 ms ✓ Setfield 1341.6 ms ✓ Distances → DistancesSparseArraysExt 5102.2 ms ✓ Accessors 1342.7 ms ✓ DifferentiationInterface → DifferentiationInterfaceSparseArraysExt 809.1 ms ✓ LogExpFunctions → LogExpFunctionsInverseFunctionsExt 1781.4 ms ✓ Tables 1160.1 ms ✓ ArrayInterface 1263.7 ms ✓ Adapt → AdaptSparseArraysExt 1568.9 ms ✓ FillArrays → FillArraysPDMatsExt 3922.9 ms ✓ DataStructures 3274.3 ms ✓ StringManipulation 13709.0 ms ✓ StaticArrays 1475.8 ms ✓ Lz4_jll 1633.5 ms ✓ Rmath_jll 1262.0 ms ✓ MicrosoftMPI_jll 1401.8 ms ✓ OpenSpecFun_jll 1419.2 ms ✓ libaec_jll 1422.0 ms ✓ Xorg_libpciaccess_jll 1395.6 ms ✓ Libiconv_jll 4595.0 ms ✓ MPItrampoline_jll 2411.3 ms ✓ Accessors → LinearAlgebraExt 1313.4 ms ✓ StableHashTraits 743.1 ms ✓ ArrayInterface → ArrayInterfaceStaticArraysCoreExt 1263.2 ms ✓ ArrayInterface → ArrayInterfaceSparseArraysExt 1522.5 ms ✓ SortingAlgorithms 2833.6 ms ✓ QuadGK 39644.0 ms ✓ PrettyTables 1550.5 ms ✓ StaticArrays → StaticArraysStatisticsExt 1409.3 ms ✓ ConstructionBase → ConstructionBaseStaticArraysExt 1478.6 ms ✓ DifferentiationInterface → DifferentiationInterfaceStaticArraysExt 1396.9 ms ✓ Adapt → AdaptStaticArraysExt 1512.4 ms ✓ Accessors → StaticArraysExt 1414.3 ms ✓ Blosc_jll 1686.8 ms ✓ Rmath 5039.1 ms ✓ SpecialFunctions 1619.4 ms ✓ XML2_jll 6790.8 ms ✓ Roots 1345.4 ms ✓ FiniteDiff 5141.1 ms ✓ StatsBase 90924.9 ms ✓ DataFrames 5044.8 ms ✓ NearestNeighbors 1119.9 ms ✓ Blosc 2406.1 ms ✓ HypergeometricFunctions 1265.9 ms ✓ DiffRules 1442.1 ms ✓ Hwloc_jll 1943.0 ms ✓ KernelDensitySJ 1391.9 ms ✓ FiniteDiff → FiniteDiffStaticArraysExt 1287.1 ms ✓ FiniteDiff → FiniteDiffSparseArraysExt 957.1 ms ✓ DifferentiationInterface → DifferentiationInterfaceFiniteDiffExt 1907.4 ms ✓ PDMats → StatsBaseExt 2838.5 ms ✓ StatsFuns 6653.3 ms ✓ ForwardDiff 4957.1 ms ✓ MPICH_jll 4713.8 ms ✓ OpenMPI_jll 1019.7 ms ✓ StatsFuns → StatsFunsInverseFunctionsExt 9587.1 ms ✓ Distributions 2127.6 ms ✓ ForwardDiff → ForwardDiffStaticArraysExt 1510.6 ms ✓ DifferentiationInterface → DifferentiationInterfaceForwardDiffExt 1378.3 ms ✓ Roots → RootsForwardDiffExt 5624.7 ms ✓ HDF5_jll 2256.9 ms ✓ NLSolversBase 14696.5 ms ✓ HDF5 2469.3 ms ✓ LineSearches 5989.5 ms ✓ SingleCell10x 5694.4 ms ✓ H5Zblosc 6769.3 ms ✓ Optim ERROR: LoadError: ArgumentError: Cannot load (`using/import`) module SHA into module SCTransform in package SCTransform because package SCTransform 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 SCTransform 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 SCTransform Stacktrace:  [1] macro expansion  @ ./loading.jl:2497 [inlined]  [2] macro expansion  @ ./lock.jl:376 [inlined]  [3] __require(into::Module, mod::Symbol)  @ Base ./loading.jl:2477  [4] require  @ ./loading.jl:2453 [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/SCTransform/OgRBw/src/SCTransform.jl:15  [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:3157  [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:3003  [15] include_string  @ ./loading.jl:3013 [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/SCTransform/OgRBw/src/SCTransform.jl:1 in expression starting at stdin:5 Precompilation completed after 421.18s ################################################################################ # Testing # Testing SingleCellProjections Status `/tmp/jl_A5nEoE/Project.toml` [1520ce14] AbstractTrees v0.4.5 [944b1d66] CodecZlib v0.7.8 [a93c6f00] DataFrames v1.8.1 [8bb1440f] DelimitedFiles v1.9.1 [31c24e10] Distributions v0.25.122 [38e38edf] GLM v1.9.0 [c8ec2601] H5Zblosc v0.1.2 [f67ccb44] HDF5 v0.17.2 [09f84164] HypothesisTests v0.11.6 [e1d29d7a] Missings v1.2.0 [b8a86587] NearestNeighbors v0.4.24 [aea7be01] PrecompileTools v1.3.3 [6a3ba550] PrincipalMomentAnalysis v0.2.2 [f56ea72b] SCTransform v0.3.1 [eddce310] SingleCell10x v0.2.2 [03d38035] SingleCellProjections v0.4.4 [860ef19b] StableRNGs v1.0.4 [90137ffa] StaticArrays v1.9.15 [10745b16] Statistics v1.11.1 [24678dba] TSne v1.3.0 [59d54670] ThreadedSparseArrays v0.2.3 [c4f8c510] UMAP v0.1.11 [37e2e46d] LinearAlgebra v1.13.0 [9a3f8284] Random v1.11.0 [2f01184e] SparseArrays v1.13.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_A5nEoE/Manifest.toml` [47edcb42] ADTypes v1.19.0 [1520ce14] AbstractTrees v0.4.5 [7d9f7c33] Accessors v0.1.42 [79e6a3ab] Adapt v4.4.0 [66dad0bd] AliasTables v1.1.3 [ec485272] ArnoldiMethod v0.4.0 [7d9fca2a] Arpack v0.5.4 [4fba245c] ArrayInterface v7.22.0 [a74b3585] Blosc v0.7.3 [944b1d66] CodecZlib v0.7.8 [861a8166] Combinatorics v1.0.3 [38540f10] CommonSolve v0.2.4 [bbf7d656] CommonSubexpressions v0.3.1 [34da2185] Compat v4.18.1 [a33af91c] CompositionsBase v0.1.2 [187b0558] ConstructionBase v1.6.0 [a8cc5b0e] Crayons v4.1.1 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.8.1 ⌅ [864edb3b] DataStructures v0.18.22 [e2d170a0] DataValueInterfaces v1.0.0 [8bb1440f] DelimitedFiles v1.9.1 [163ba53b] DiffResults v1.1.0 [b552c78f] DiffRules v1.15.1 [a0c0ee7d] DifferentiationInterface v0.7.12 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.122 [ffbed154] DocStringExtensions v0.9.5 [4e289a0a] EnumX v1.0.5 [1a297f60] FillArrays v1.15.0 [6a86dc24] FiniteDiff v2.29.0 [f6369f11] ForwardDiff v1.3.0 [38e38edf] GLM v1.9.0 [86223c79] Graphs v1.13.1 [c8ec2601] H5Zblosc v0.1.2 [f67ccb44] HDF5 v0.17.2 [34004b35] HypergeometricFunctions v0.3.28 [09f84164] HypothesisTests v0.11.6 [d25df0c9] Inflate v0.1.5 [842dd82b] InlineStrings v1.4.5 [3587e190] InverseFunctions v0.1.17 [41ab1584] InvertedIndices v1.3.1 [92d709cd] IrrationalConstants v0.2.6 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.7.1 [49dc5b4e] KernelDensitySJ v0.2.1 [b964fa9f] LaTeXStrings v1.4.0 [d3d80556] LineSearches v7.5.1 [2ab3a3ac] LogExpFunctions v0.3.29 [2fda8390] LsqFit v0.15.1 [3da0fdf6] MPIPreferences v0.1.11 [1914dd2f] MacroTools v0.5.16 [e1d29d7a] Missings v1.2.0 [d41bc354] NLSolversBase v7.10.0 [77ba4419] NaNMath v1.1.3 [dd2c4c9e] NearestNeighborDescent v0.3.7 [b8a86587] NearestNeighbors v0.4.24 [429524aa] Optim v1.13.3 [bac558e1] OrderedCollections v1.8.1 [90014a1f] PDMats v0.11.36 [2dfb63ee] PooledArrays v1.4.3 [85a6dd25] PositiveFactorizations v0.2.4 [aea7be01] PrecompileTools v1.3.3 [21216c6a] Preferences v1.5.0 [08abe8d2] PrettyTables v3.1.2 [6a3ba550] PrincipalMomentAnalysis v0.2.2 [92933f4c] ProgressMeter v1.11.0 [43287f4e] PtrArrays v1.3.0 [1fd47b50] QuadGK v2.11.2 [189a3867] Reexport v1.2.2 [ae029012] Requires v1.3.1 [79098fc4] Rmath v0.9.0 [f2b01f46] Roots 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[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 v1.13.0 [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 v8.17.0+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 ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... ERROR: LoadError: ArgumentError: Cannot load (`using/import`) module SHA into module SCTransform in package SCTransform because package SCTransform 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:  /tmp/jl_A5nEoE/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 SCTransform 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 SCTransform Stacktrace:  [1] macro expansion  @ ./loading.jl:2497 [inlined]  [2] macro expansion  @ ./lock.jl:376 [inlined]  [3] __require(into::Module, mod::Symbol)  @ Base ./loading.jl:2477  [4] require  @ ./loading.jl:2453 [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/SCTransform/OgRBw/src/SCTransform.jl:15  [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:3157  [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:3003  [15] include_string  @ ./loading.jl:3013 [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/SCTransform/OgRBw/src/SCTransform.jl:1 in expression starting at stdin:5 ERROR: LoadError: ArgumentError: Cannot load (`using/import`) module SHA into module SCTransform in package SCTransform because package SCTransform 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:  /tmp/jl_A5nEoE/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 SCTransform 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 SCTransform Stacktrace:  [1] macro expansion  @ ./loading.jl:2497 [inlined]  [2] macro expansion  @ ./lock.jl:376 [inlined]  [3] __require(into::Module, mod::Symbol)  @ Base ./loading.jl:2477  [4] require  @ ./loading.jl:2453 [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/SCTransform/OgRBw/src/SCTransform.jl:15  [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:3157  [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:3003  [15] include_string  @ ./loading.jl:3013 [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/SCTransform/OgRBw/src/SCTransform.jl:1 in expression starting at stdin:5 1 dependency had output during precompilation: ┌ SCTransform │ [Output was shown above] └ ERROR: LoadError: The following 1 package failed to precompile: SCTransform Failed to precompile SCTransform [f56ea72b-d1ea-403e-9c0c-95d94e8a8532] to "/home/pkgeval/.julia/compiled/v1.14/SCTransform/jl_dF3yz2" (ProcessExited(1)). in expression starting at /home/pkgeval/.julia/packages/SingleCellProjections/30C4U/src/SingleCellProjections.jl:1 in expression starting at /home/pkgeval/.julia/packages/SingleCellProjections/30C4U/test/runtests.jl:1 Testing failed after 69.13s ERROR: LoadError: Package SingleCellProjections errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Types.jl:68 [2] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, julia_args::Cmd, test_args::Cmd, test_fn::Nothing, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool) @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:2946 [3] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:2795 [inlined] [4] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool, kwargs::@Kwargs{io::IOContext{IO}}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:572 [5] kwcall(::@NamedTuple{julia_args::Cmd, io::IOContext{IO}}, ::typeof(Pkg.API.test), ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:548 [6] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:172 [7] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:161 [8] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [9] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [inlined] [10] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkg::String) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [11] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:219 [12] include(mod::Module, _path::String) @ Base ./Base.jl:309 [13] exec_options(opts::Base.JLOptions) @ Base ./client.jl:344 [14] _start() @ Base ./client.jl:577 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 555.08s: package fails to precompile