Package evaluation to test SingleCellProjections on Julia 1.14.0-DEV.65 (b05afe0f25*) started at 2025-11-12T01:10:12.705 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 7.91s ################################################################################ # 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 ForwardDiff ───────────────── v1.2.2 Installed DataStructures ────────────── v0.18.22 Installed StableHashTraits ──────────── v2.0.2 Installed Lz4_jll ───────────────────── v1.10.1+0 Installed FillArrays ────────────────── v1.15.0 Installed AbstractTrees ─────────────── v0.4.5 Installed libaec_jll ────────────────── v1.1.4+0 Installed Adapt ─────────────────────── v4.4.0 Installed InlineStrings ─────────────── v1.4.5 Installed SCTransform ───────────────── v0.3.1 Installed MPICH_jll ─────────────────── v4.3.2+0 Installed HypergeometricFunctions ───── v0.3.28 Installed ConstructionBase ──────────── v1.6.0 Installed DelimitedFiles ────────────── v1.9.1 Installed SingleCellProjections ─────── v0.4.4 Installed AliasTables ───────────────── v1.1.3 Installed CodecZlib ─────────────────── v0.7.8 Installed MicrosoftMPI_jll ──────────── v10.1.4+3 Installed StatsBase ─────────────────── v0.34.8 Installed ArrayInterface ────────────── v7.22.0 Installed OrderedCollections ────────── v1.8.1 Installed TranscodingStreams ────────── v0.11.3 Installed Optim ─────────────────────── v1.13.2 Installed NearestNeighbors ──────────── v0.4.22 Installed IteratorInterfaceExtensions ─ v1.0.0 Installed Compat ────────────────────── v4.18.1 Installed InvertedIndices ───────────── v1.3.1 Installed DataAPI ───────────────────── v1.16.0 Installed PositiveFactorizations ────── v0.2.4 Installed Statistics ────────────────── v1.11.1 Installed Blosc ─────────────────────── v0.7.3 Installed PrecompileTools ───────────── v1.3.3 Installed Xorg_libpciaccess_jll ─────── v0.18.1+0 Installed DataValueInterfaces ───────── v1.0.0 Installed StatsAPI ──────────────────── v1.7.1 Installed SentinelArrays ────────────── v1.4.8 Installed ProgressMeter ─────────────── v1.11.0 Installed CommonSubexpressions ──────── v0.3.1 Installed Blosc_jll ─────────────────── v1.21.7+0 Installed SingleCell10x ─────────────── v0.2.2 Installed StaticArrays ──────────────── v1.9.15 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 ────────── v0.4.1 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 ───────────────── v5.0.8+0 Installed Roots ─────────────────────── v2.2.10 Installed ThreadedSparseArrays ──────── v0.2.3 Installed Hwloc_jll ─────────────────── v2.12.2+0 Installed PrettyTables ──────────────── v3.1.0 Installed FiniteDiff ────────────────── v2.29.0 Installed Rmath ─────────────────────── v0.9.0 Installed Parameters ────────────────── v0.12.3 Installed Distributions ─────────────── v0.25.122 Installed StatsFuns ─────────────────── v1.5.2 Installed Tables ────────────────────── v1.12.1 Installed PtrArrays ─────────────────── v1.3.0 Installed XML2_jll ──────────────────── v2.13.9+0 Installed EnumX ─────────────────────── v1.0.5 Installed NLSolversBase ─────────────── v7.10.0 Installed Scratch ───────────────────── v1.3.0 Installed InverseFunctions ──────────── v0.1.17 Installed SpecialFunctions ──────────── v2.6.1 Installed Reexport ──────────────────── v1.2.2 Installed DataFrames ────────────────── v1.8.1 Installed H5Zblosc ──────────────────── v0.1.2 Installed Setfield ──────────────────── v1.1.2 Installed Missings ──────────────────── v1.2.0 Installed Preferences ───────────────── v1.5.0 Installed MPIPreferences ────────────── v0.1.11 Installed PooledArrays ──────────────── v1.4.3 Installed JLLWrappers ───────────────── v1.7.1 Installed TableTraits ───────────────── v1.0.1 Installed Libiconv_jll ──────────────── v1.18.0+0 Installed LaTeXStrings ──────────────── v1.4.0 Installed SortingAlgorithms ─────────── v1.2.2 Installed LineSearches ──────────────── v7.4.0 Installed KernelDensitySJ ───────────── v0.2.1 Installed PDMats ────────────────────── v0.11.36 Installed Crayons ───────────────────── v4.1.1 Installed StructTypes ───────────────── v1.11.0 Installed HDF5 ──────────────────────── v0.17.2 Installed MPItrampoline_jll ─────────── v5.5.4+0 Installed UnPack ────────────────────── v1.0.2 Installed ADTypes ───────────────────── v1.18.0 Installed Accessors ─────────────────── v0.1.42 Installed DocStringExtensions ───────── v0.9.5 Installed DifferentiationInterface ──── v0.7.11 Installing 11 artifacts Installed artifact Blosc 44.2 KiB Installed artifact Rmath 121.9 KiB Installed artifact Lz4 239.7 KiB Installed artifact Xorg_libpciaccess 24.8 KiB Installed artifact libaec 49.6 KiB Installed artifact OpenSpecFun 194.9 KiB Installed artifact XML2 2.5 MiB Installed artifact Hwloc 3.5 MiB Installed artifact MPICH 3.3 MiB Installed artifact Libiconv 1.9 MiB Installed artifact HDF5 5.7 MiB Updating `~/.julia/environments/v1.14/Project.toml` [03d38035] + SingleCellProjections v0.4.4 Updating `~/.julia/environments/v1.14/Manifest.toml` [47edcb42] + ADTypes v1.18.0 [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 v0.7.11 [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 v1.2.2 [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 v7.4.0 [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 v0.4.22 [429524aa] + Optim v1.13.2 [bac558e1] + OrderedCollections v1.8.1 [90014a1f] + PDMats v0.11.36 [d96e819e] + Parameters v0.12.3 [2dfb63ee] + PooledArrays v1.4.3 [85a6dd25] + PositiveFactorizations v0.2.4 [aea7be01] + PrecompileTools v1.3.3 [21216c6a] + Preferences v1.5.0 [08abe8d2] + PrettyTables v3.1.0 [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 v0.4.1 [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 [3a884ed6] + UnPack v1.0.2 [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 v5.0.8+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 v1.11.0 [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 v8.16.0+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 ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Installation completed after 15.97s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... WARNING: Imported binding Operations.project_rel_path was undeclared at import time during import to TestEnv. 4159.4 ms ✓ TestEnv 1 dependency successfully precompiled in 4 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/nGMfF/src/julia-1.11/common.jl:75 │ [2] test_dir_has_project_file │ @ ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/common.jl:52 [inlined] │ [3] maybe_gen_project_override! │ @ ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/common.jl:83 [inlined] │ [4] activate(pkg::String; allow_reresolve::Bool) │ @ TestEnv ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/activate_set.jl:12 │ [5] activate(pkg::String) │ @ TestEnv ~/.julia/packages/TestEnv/nGMfF/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... 4539.8 ms ✓ MacroTools 1728.0 ms ✓ InlineStrings 992.2 ms ✓ Reexport 1165.2 ms ✓ ConstructionBase 2306.9 ms ✓ IrrationalConstants 849.4 ms ✓ DataValueInterfaces 860.6 ms ✓ StatsAPI 1011.6 ms ✓ TupleTools 829.3 ms ✓ CommonSolve 1349.3 ms ✓ TranscodingStreams 934.2 ms ✓ LaTeXStrings 1280.2 ms ✓ Statistics 1034.5 ms ✓ StaticArraysCore 1028.5 ms ✓ PtrArrays 892.2 ms ✓ PositiveFactorizations 859.2 ms ✓ DataAPI 847.9 ms ✓ InvertedIndices 946.2 ms ✓ InverseFunctions 823.0 ms ✓ CompositionsBase 1094.2 ms ✓ AbstractTrees 865.0 ms ✓ EnumX 2464.2 ms ✓ FillArrays 817.7 ms ✓ UnPack 1267.4 ms ✓ OrderedCollections 1370.2 ms ✓ ADTypes 1097.6 ms ✓ DocStringExtensions 748.8 ms ✓ IteratorInterfaceExtensions 2132.0 ms ✓ Crayons 1023.3 ms ✓ DelimitedFiles 1058.0 ms ✓ NaNMath 1177.2 ms ✓ Requires 1247.9 ms ✓ SuiteSparse 1628.6 ms ✓ ThreadedSparseArrays 950.1 ms ✓ Scratch 3360.6 ms ✓ SentinelArrays 1682.1 ms ✓ StructTypes 1889.8 ms ✓ ProgressMeter 1204.3 ms ✓ Compat 1193.5 ms ✓ Preferences 1875.5 ms ✓ CommonSubexpressions 837.3 ms ✓ ConstructionBase → ConstructionBaseLinearAlgebraExt 1015.5 ms ✓ CodecZlib 1327.2 ms ✓ Statistics → SparseArraysExt 1523.2 ms ✓ Distances 904.1 ms ✓ DiffResults 991.9 ms ✓ AliasTables 1017.8 ms ✓ Missings 1056.1 ms ✓ PooledArrays 873.9 ms ✓ InverseFunctions → InverseFunctionsDatesExt 853.3 ms ✓ CompositionsBase → CompositionsBaseInverseFunctionsExt 1520.3 ms ✓ FillArrays → FillArraysSparseArraysExt 977.7 ms ✓ FillArrays → FillArraysStatisticsExt 973.5 ms ✓ Parameters 792.0 ms ✓ ADTypes → ADTypesConstructionBaseExt 1975.6 ms ✓ DifferentiationInterface 1707.1 ms ✓ LogExpFunctions 876.2 ms ✓ TableTraits 998.1 ms ✓ Adapt 1835.7 ms ✓ PDMats 867.0 ms ✓ Compat → CompatLinearAlgebraExt 1014.0 ms ✓ PrecompileTools 1389.2 ms ✓ JLLWrappers 1503.1 ms ✓ MPIPreferences 3333.1 ms ✓ Setfield 1319.3 ms ✓ Distances → DistancesSparseArraysExt 5370.4 ms ✓ Accessors 1358.2 ms ✓ DifferentiationInterface → DifferentiationInterfaceSparseArraysExt 849.4 ms ✓ LogExpFunctions → LogExpFunctionsInverseFunctionsExt 1822.3 ms ✓ Tables 1189.1 ms ✓ ArrayInterface 1308.1 ms ✓ Adapt → AdaptSparseArraysExt 1508.0 ms ✓ FillArrays → FillArraysPDMatsExt 4140.6 ms ✓ DataStructures 2918.6 ms ✓ StringManipulation 15096.9 ms ✓ StaticArrays 1533.1 ms ✓ Lz4_jll 1469.4 ms ✓ Rmath_jll 1203.6 ms ✓ MicrosoftMPI_jll 1417.2 ms ✓ OpenSpecFun_jll 1393.1 ms ✓ libaec_jll 1283.1 ms ✓ Xorg_libpciaccess_jll 1437.5 ms ✓ Libiconv_jll 4718.4 ms ✓ MPItrampoline_jll 2693.5 ms ✓ Accessors → LinearAlgebraExt 1383.8 ms ✓ StableHashTraits 794.9 ms ✓ ArrayInterface → ArrayInterfaceStaticArraysCoreExt 1325.3 ms ✓ ArrayInterface → ArrayInterfaceSparseArraysExt 1623.1 ms ✓ SortingAlgorithms 2972.4 ms ✓ QuadGK 42300.9 ms ✓ PrettyTables 1422.3 ms ✓ StaticArrays → StaticArraysStatisticsExt 1468.9 ms ✓ ConstructionBase → ConstructionBaseStaticArraysExt 1463.5 ms ✓ DifferentiationInterface → DifferentiationInterfaceStaticArraysExt 1417.3 ms ✓ Adapt → AdaptStaticArraysExt 1574.1 ms ✓ Accessors → StaticArraysExt 1468.3 ms ✓ Blosc_jll 1495.6 ms ✓ Rmath 5418.3 ms ✓ SpecialFunctions 1510.7 ms ✓ XML2_jll 7342.2 ms ✓ Roots 1358.8 ms ✓ FiniteDiff 5172.3 ms ✓ StatsBase 100931.2 ms ✓ DataFrames 4685.2 ms ✓ NearestNeighbors 1098.1 ms ✓ Blosc 2583.8 ms ✓ HypergeometricFunctions 1312.6 ms ✓ DiffRules 1493.4 ms ✓ Hwloc_jll 2001.1 ms ✓ KernelDensitySJ 1444.0 ms ✓ FiniteDiff → FiniteDiffStaticArraysExt 1297.1 ms ✓ FiniteDiff → FiniteDiffSparseArraysExt 967.2 ms ✓ DifferentiationInterface → DifferentiationInterfaceFiniteDiffExt 1904.6 ms ✓ PDMats → StatsBaseExt 2980.2 ms ✓ StatsFuns 6963.9 ms ✓ ForwardDiff 5525.1 ms ✓ MPICH_jll 4678.2 ms ✓ OpenMPI_jll 1036.0 ms ✓ StatsFuns → StatsFunsInverseFunctionsExt 10011.2 ms ✓ Distributions 2047.4 ms ✓ ForwardDiff → ForwardDiffStaticArraysExt 1543.1 ms ✓ DifferentiationInterface → DifferentiationInterfaceForwardDiffExt 1430.7 ms ✓ Roots → RootsForwardDiffExt 5531.3 ms ✓ HDF5_jll 2274.7 ms ✓ NLSolversBase 15977.9 ms ✓ HDF5 4919.9 ms ✓ LineSearches 6309.7 ms ✓ SingleCell10x 5393.5 ms ✓ H5Zblosc 7187.6 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:2491 [inlined]  [2] macro expansion  @ ./lock.jl:376 [inlined]  [3] __require(into::Module, mod::Symbol)  @ Base ./loading.jl:2471  [4] require  @ ./loading.jl:2447 [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:3151  [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:2997  [15] include_string  @ ./loading.jl:3007 [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 445.73s ################################################################################ # Testing # Testing SingleCellProjections Status `/tmp/jl_pyWSXW/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 v0.4.22 [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_pyWSXW/Manifest.toml` [47edcb42] ADTypes v1.18.0 [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 v0.7.11 [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 v1.2.2 [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 v7.4.0 [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 v0.4.22 [429524aa] Optim v1.13.2 [bac558e1] OrderedCollections v1.8.1 [90014a1f] PDMats v0.11.36 [d96e819e] Parameters v0.12.3 [2dfb63ee] PooledArrays v1.4.3 [85a6dd25] PositiveFactorizations v0.2.4 [aea7be01] PrecompileTools v1.3.3 [21216c6a] Preferences v1.5.0 [08abe8d2] PrettyTables v3.1.0 [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 v2.2.10 [f56ea72b] SCTransform v0.3.1 [6c6a2e73] Scratch v1.3.0 [91c51154] SentinelArrays v1.4.8 [efcf1570] Setfield v1.1.2 [1277b4bf] ShiftedArrays v2.0.0 [699a6c99] SimpleTraits v0.9.5 [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 [860ef19b] StableRNGs v1.0.4 [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 [3eaba693] StatsModels v0.7.7 [892a3eda] StringManipulation v0.4.1 [856f2bd8] StructTypes v1.11.0 [24678dba] TSne v1.3.0 [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 [c4f8c510] UMAP v0.1.11 [3a884ed6] UnPack v1.0.2 ⌅ [68821587] Arpack_jll v3.5.1+1 [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 v5.0.8+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 [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 ⌅ 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_pyWSXW/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:2491 [inlined]  [2] macro expansion  @ ./lock.jl:376 [inlined]  [3] __require(into::Module, mod::Symbol)  @ Base ./loading.jl:2471  [4] require  @ ./loading.jl:2447 [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:3151  [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:2997  [15] include_string  @ ./loading.jl:3007 [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_pyWSXW/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:2491 [inlined]  [2] macro expansion  @ ./lock.jl:376 [inlined]  [3] __require(into::Module, mod::Symbol)  @ Base ./loading.jl:2471  [4] require  @ ./loading.jl:2447 [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:3151  [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:2997  [15] include_string  @ ./loading.jl:3007 [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_qMA6TU" (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 72.25s 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 587.29s: package fails to precompile